Exomiser Analysis Results for Anonymous
Analysis Settings
Settings used for this analysis:
---
sample:
genomeAssembly: "hg19"
vcf: "/exomiser/challenge02.vcf.gz"
hpoIds:
- "HP:0001156"
- "HP:0001363"
- "HP:0011304"
- "HP:0010055"
pedigree: {}
age: {}
analysis:
inheritanceModes:
AUTOSOMAL_RECESSIVE_COMP_HET: 2.0
MITOCHONDRIAL: 0.2
AUTOSOMAL_RECESSIVE_HOM_ALT: 0.1
X_DOMINANT: 0.1
AUTOSOMAL_DOMINANT: 0.1
X_RECESSIVE_COMP_HET: 2.0
X_RECESSIVE_HOM_ALT: 0.1
frequencySources:
- "THOUSAND_GENOMES"
- "TOPMED"
- "UK10K"
- "ESP_AFRICAN_AMERICAN"
- "ESP_EUROPEAN_AMERICAN"
- "ESP_ALL"
- "EXAC_AFRICAN_INC_AFRICAN_AMERICAN"
- "EXAC_AMERICAN"
- "EXAC_EAST_ASIAN"
- "EXAC_FINNISH"
- "EXAC_NON_FINNISH_EUROPEAN"
- "EXAC_OTHER"
- "EXAC_SOUTH_ASIAN"
- "GNOMAD_E_AFR"
- "GNOMAD_E_AMR"
- "GNOMAD_E_EAS"
- "GNOMAD_E_FIN"
- "GNOMAD_E_NFE"
- "GNOMAD_E_OTH"
- "GNOMAD_E_SAS"
- "GNOMAD_G_AFR"
- "GNOMAD_G_AMR"
- "GNOMAD_G_EAS"
- "GNOMAD_G_FIN"
- "GNOMAD_G_NFE"
- "GNOMAD_G_OTH"
- "GNOMAD_G_SAS"
pathogenicitySources:
- "POLYPHEN"
- "MUTATION_TASTER"
- "SIFT"
steps:
- variantEffectFilter:
remove:
- "CODING_TRANSCRIPT_INTRON_VARIANT"
- "FIVE_PRIME_UTR_EXON_VARIANT"
- "THREE_PRIME_UTR_EXON_VARIANT"
- "FIVE_PRIME_UTR_INTRON_VARIANT"
- "THREE_PRIME_UTR_INTRON_VARIANT"
- "NON_CODING_TRANSCRIPT_EXON_VARIANT"
- "NON_CODING_TRANSCRIPT_INTRON_VARIANT"
- "UPSTREAM_GENE_VARIANT"
- "DOWNSTREAM_GENE_VARIANT"
- "INTERGENIC_VARIANT"
- "REGULATORY_REGION_VARIANT"
- frequencyFilter:
maxFrequency: 2.0
- pathogenicityFilter:
keepNonPathogenic: true
- inheritanceFilter: {}
- omimPrioritiser: {}
- hiPhivePrioritiser:
runParams: "human, mouse, fish, ppi"
outputOptions:
outputPrefix: "results/Pfeiffer-hiphive-exome-PASS_ONLY"
outputFormats:
- "HTML"
- "VCF"
- "TSV_GENE"
- "TSV_VARIANT"
- "JSON"
Filtering Summary
| Filter | Report | Passed filter | Failed filter |
|---|---|---|---|
| Variant effect |
|
1081 | 0 |
| Frequency |
|
1081 | 0 |
| Pathogenicity |
|
1081 | 0 |
| Inheritance |
|
418 | 0 |
Variant Type Distribution
| Variant Type | sample |
|---|---|
| FRAMESHIFT_ELONGATION | 16 |
| FRAMESHIFT_TRUNCATION | 16 |
| FRAMESHIFT_VARIANT | 11 |
| INTERNAL_FEATURE_ELONGATION | 0 |
| FEATURE_TRUNCATION | 0 |
| MNV | 0 |
| STOP_GAINED | 19 |
| STOP_LOST | 1 |
| START_LOST | 1 |
| SPLICE_ACCEPTOR_VARIANT | 8 |
| SPLICE_DONOR_VARIANT | 11 |
| MISSENSE_VARIANT | 602 |
| INFRAME_INSERTION | 6 |
| DISRUPTIVE_INFRAME_INSERTION | 11 |
| INFRAME_DELETION | 6 |
| DISRUPTIVE_INFRAME_DELETION | 9 |
| FIVE_PRIME_UTR_TRUNCATION | 0 |
| THREE_PRIME_UTR_TRUNCATION | 0 |
| SPLICE_REGION_VARIANT | 86 |
| STOP_RETAINED_VARIANT | 0 |
| INITIATOR_CODON_VARIANT | 0 |
| SYNONYMOUS_VARIANT | 278 |
| CODING_TRANSCRIPT_INTRON_VARIANT | 0 |
| THREE_PRIME_UTR_EXON_VARIANT | 0 |
| FIVE_PRIME_UTR_INTRON_VARIANT | 0 |
| THREE_PRIME_UTR_INTRON_VARIANT | 0 |
| NON_CODING_TRANSCRIPT_EXON_VARIANT | 0 |
| NON_CODING_TRANSCRIPT_INTRON_VARIANT | 0 |
| UPSTREAM_GENE_VARIANT | 0 |
| DOWNSTREAM_GENE_VARIANT | 0 |
| INTERGENIC_VARIANT | 0 |
| REGULATORY_REGION_VARIANT | 0 |
Prioritised Genes
- Phenotypic similarity 0.869 to Non-specific syndromic intellectual disability associated with BCORL1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010109, Short hallux
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0011304, Broad thumb
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
- Proximity score 0.501 in interactome to HDAC4 and phenotypic similarity 0.656 to 2q37 microdeletion syndrome associated with HDAC4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0002007, Frontal bossing
- HP:0011304, Broad thumb - HP:0006101, Finger syndactyly
- HP:0010055, Broad hallux - HP:0001770, Toe syndactyly
- Proximity score 0.501 in interactome to HDAC4 and phenotypic similarity 0.934 to mouse mutant of HDAC4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000165, abnormal long bone hypertrophic chondrocyte zone
- HP:0001363, Craniosynostosis - MP:0030356, premature lambdoid suture closure
- HP:0011304, Broad thumb - MP:0000165, abnormal long bone hypertrophic chondrocyte zone
- HP:0010055, Broad hallux - MP:0000165, abnormal long bone hypertrophic chondrocyte zone
- Proximity score 0.501 in interactome to HDAC4 and phenotypic similarity 0.614 to fish mutant of HDAC4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - ZP:0107238, anguloarticular premature ossification, abnormal
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Known diseases:
- OMIM:301029 Shukla-Vernon syndrome - X-linked recessive
- ORPHA:528084 Non-specific syndromic intellectual disability - X-linked recessive
X_RECESSIVE
Exomiser Score: 0.984
Phenotype Score: 0.869
Variant Score: 0.910
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.869 to ORPHA:528084 Non-specific syndromic intellectual disability
- Phenotypic similarity 0.432 to OMIM:301029 Shukla-Vernon syndrome
- Pathogenicity Data:
- Best Score: 0.996
- Mutation Taster: 0.865
- SIFT: 0.004 (D)
- Frequency Data:
- 1000Genomes: 0.0530%
- TOPMed: 0.0302%
- ExAC EAS: 0.3767%
- gnomAD_E_EAS: 0.4429%
- gnomAD_G_EAS: 0.4936%
- Phenotypic similarity 0.744 to mouse mutant involving CPLANE2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000562, polydactyly
- HP:0001363, Craniosynostosis - MP:0002639, micrognathia
- HP:0011304, Broad thumb - MP:0000562, polydactyly
- HP:0010055, Broad hallux - MP:0000562, polydactyly
- Proximity score 0.539 in interactome to FUZ and phenotypic similarity 0.251 to Caudal regression sequence associated with FUZ.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0000921, Missing ribs
- HP:0010055, Broad hallux - HP:0001762, Talipes equinovarus
- Proximity score 0.539 in interactome to FUZ and phenotypic similarity 0.752 to mouse mutant of FUZ.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000562, polydactyly
- HP:0001363, Craniosynostosis - MP:0001293, anophthalmia
- HP:0011304, Broad thumb - MP:0000562, polydactyly
- HP:0010055, Broad hallux - MP:0000562, polydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.974
Phenotype Score: 0.744
Variant Score: 1.000
- Transcripts:
- CPLANE2:ENST00000375599.3:c.260C>G:p.(Thr87Ser)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.367 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.734 to mouse mutant involving BAIAP2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000565, oligodactyly
- HP:0001363, Craniosynostosis - MP:0000079, abnormal basioccipital bone morphology
- HP:0011304, Broad thumb - MP:0000565, oligodactyly
- HP:0010055, Broad hallux - MP:0000565, oligodactyly
- Proximity score 0.501 in interactome to ACTB and phenotypic similarity 0.706 to Baraitser-Winter cerebrofrontofacial syndrome associated with ACTB.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0009942, Duplication of thumb phalanx
- HP:0001363, Craniosynostosis - HP:0005487, Prominent metopic ridge
- HP:0011304, Broad thumb - HP:0009942, Duplication of thumb phalanx
- HP:0010055, Broad hallux - HP:0009942, Duplication of thumb phalanx
- Proximity score 0.501 in interactome to ACTB and phenotypic similarity 0.239 to mouse mutant of ACTB.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0004527, abnormal outer hair cell stereociliary bundle morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.971
Phenotype Score: 0.734
Variant Score: 1.000
- Transcripts:
- BAIAP2:ENST00000321280.7:c.1558A>G:p.(Thr520Ala)
- BAIAP2:ENST00000321300.6:c.1535+481A>G:p.(=)
- BAIAP2:ENST00000392411.3:c.1301+481A>G:p.(=)
- BAIAP2:ENST00000428708.2:c.1535+481A>G:p.(=)
- BAIAP2:ENST00000435091.3:c.1535+481A>G:p.(=)
- BAIAP2:ENST00000575245.1:c.1634+481A>G:p.(=)
- BAIAP2:ENST00000575712.1:c.*477A>G:p.(=)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.971 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.479 to Primary ciliary dyskinesia associated with HYDIN.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001217, Clubbing
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001217, Clubbing
- HP:0010055, Broad hallux - HP:0001217, Clubbing
- Phenotypic similarity 0.652 to mouse mutant involving HYDIN.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0030029, wide cranial sutures
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.502 in interactome to IFT80 and phenotypic similarity 0.662 to Jeune syndrome associated with IFT80.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001162, Postaxial hand polydactyly
- HP:0010055, Broad hallux - HP:0001770, Toe syndactyly
- Proximity score 0.502 in interactome to IFT80 and phenotypic similarity 0.702 to mouse mutant of IFT80.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0009743, preaxial polydactyly
- HP:0001363, Craniosynostosis - MP:0000438, abnormal cranium morphology
- HP:0011304, Broad thumb - MP:0009743, preaxial polydactyly
- HP:0010055, Broad hallux - MP:0009743, preaxial polydactyly
- Known diseases:
- OMIM:608647 Ciliary dyskinesia, primary, 5 - autosomal recessive
- ORPHA:244 Primary ciliary dyskinesia - autosomal recessive
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.935
Phenotype Score: 0.652
Variant Score: 1.000
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.479 to ORPHA:244 Primary ciliary dyskinesia
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- Frequency Data:
- No frequency data
AUTOSOMAL_DOMINANT
Exomiser Score: 0.328
Phenotype Score: 0.326
Variant Score: 1.000
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000321489.5:c.2170A>G:p.(Asn724Asp)
- HYDIN:ENST00000393567.2:c.2170A>G:p.(Asn724Asp)
- HYDIN:ENST00000448089.2:c.2170A>G:p.(Asn724Asp)
- HYDIN:ENST00000448691.1:c.2170A>G:p.(Asn724Asp)
- HYDIN:ENST00000538248.1:c.2251A>G:p.(Asn751Asp)
- HYDIN:ENST00000541601.1:c.2221A>G:p.(Asn741Asp)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 1.000 (D)
- Mutation Taster: 0.971 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000288168.10:c.1517G>A:p.(Gly506Asp)
- HYDIN:ENST00000321489.5:c.1466G>A:p.(Gly489Asp)
- HYDIN:ENST00000393550.2:c.1466G>A:p.(Gly489Asp)
- HYDIN:ENST00000393567.2:c.1466G>A:p.(Gly489Asp)
- HYDIN:ENST00000448089.2:c.1466G>A:p.(Gly489Asp)
- HYDIN:ENST00000448691.1:c.1466G>A:p.(Gly489Asp)
- HYDIN:ENST00000538248.1:c.1547G>A:p.(Gly516Asp)
- HYDIN:ENST00000541601.1:c.1517G>A:p.(Gly506Asp)
- Pathogenicity Data:
- Best Score: 0.999923
- Polyphen2: 0.995 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.006 (D)
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.9347C>G:p.(Thr3116Arg)
- Pathogenicity Data:
- Best Score: 0.996
- Mutation Taster: 0.597
- SIFT: 0.004 (D)
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.11695G>A:p.(Val3899Met)
- Pathogenicity Data:
- Best Score: 0.995
- SIFT: 0.005 (D)
- Frequency Data:
- gnomAD_E_SAS: 0.0065%
- Transcripts:
- HYDIN:ENST00000393567.2:c.9947T>C:p.(Leu3316Pro)
- Pathogenicity Data:
- Best Score: 0.994072
- Mutation Taster: 0.994 (P)
- SIFT: 1.000 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.6892C>G:p.(Arg2298Gly)
- Pathogenicity Data:
- Best Score: 0.983
- Mutation Taster: 0.954 (P)
- SIFT: 0.017 (D)
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.6259C>T:p.(Arg2087Cys)
- Pathogenicity Data:
- Best Score: 0.99982
- Mutation Taster: 1.000 (P)
- SIFT: 0.001 (D)
- Frequency Data:
- 1000Genomes: 0.0399%
- TOPMed: 0.0151%
- gnomAD_E_EAS: 0.0232%
- gnomAD_G_EAS: 0.1235%
- gnomAD_G_NFE: 0.0067%
- Transcripts:
- HYDIN:ENST00000393567.2:c.12478G>C:p.(Glu4160Gln)
- Pathogenicity Data:
- Best Score: 0.971
- SIFT: 0.029 (D)
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.11224G>A:p.(Val3742Ile)
- Pathogenicity Data:
- Best Score: 0.944
- SIFT: 0.056 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.12013A>G:p.(Thr4005Ala)
- Pathogenicity Data:
- Best Score: 0.949
- Mutation Taster: 0.937
- SIFT: 0.051 (D)
- Frequency Data:
- gnomAD_E_AMR: 0.0032%
- gnomAD_E_NFE: 0.0009%
- gnomAD_G_AFR: 0.3475%
- gnomAD_G_AMR: 0.4587%
- gnomAD_G_EAS: 0.0714%
- gnomAD_G_FIN: 0.5756%
- gnomAD_G_NFE: 0.1181%
- gnomAD_G_OTH: 0.3788%
- Transcripts:
- HYDIN:ENST00000288168.10:c.2119A>G:p.(Thr707Ala)
- HYDIN:ENST00000321489.5:c.2068A>G:p.(Thr690Ala)
- HYDIN:ENST00000393550.2:c.2113A>G:p.(Thr705Ala)
- HYDIN:ENST00000393567.2:c.2068A>G:p.(Thr690Ala)
- HYDIN:ENST00000448089.2:c.2068A>G:p.(Thr690Ala)
- HYDIN:ENST00000448691.1:c.2068A>G:p.(Thr690Ala)
- HYDIN:ENST00000538248.1:c.2149A>G:p.(Thr717Ala)
- HYDIN:ENST00000541601.1:c.2119A>G:p.(Thr707Ala)
- Pathogenicity Data:
- Best Score: 0.967
- Polyphen2: 0.491 (P)
- Mutation Taster: 0.947 (P)
- SIFT: 0.033 (D)
- Frequency Data:
- gnomAD_E_AFR: 0.1663%
- gnomAD_E_AMR: 0.0756%
- gnomAD_E_EAS: 0.0945%
- gnomAD_E_NFE: 0.0289%
- gnomAD_E_OTH: 0.0554%
- gnomAD_E_SAS: 0.0328%
- gnomAD_G_AFR: 0.7378%
- gnomAD_G_EAS: 0.3708%
- gnomAD_G_FIN: 0.2583%
- gnomAD_G_NFE: 0.3007%
- gnomAD_G_OTH: 0.3074%
- Transcripts:
- HYDIN:ENST00000393567.2:c.10367+7A>G:p.?
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.4510+4G>C:p.?
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000288168.10:c.1789+8G>A:p.?
- HYDIN:ENST00000321489.5:c.1738+8G>A:p.?
- HYDIN:ENST00000393550.2:c.1738+8G>A:p.?
- HYDIN:ENST00000393567.2:c.1738+8G>A:p.?
- HYDIN:ENST00000448089.2:c.1738+8G>A:p.?
- HYDIN:ENST00000448691.1:c.1738+8G>A:p.?
- HYDIN:ENST00000538248.1:c.1819+8G>A:p.?
- HYDIN:ENST00000541601.1:c.1789+8G>A:p.?
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.12130-5G>C:p.?
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_G_AFR: 0.0470%
- Pathogenicity Data:
- Best Score: 0.759
- SIFT: 0.241 (T)
- Frequency Data:
- 1000Genomes: 0.0399%
- TOPMed: 0.0399%
- gnomAD_E_AMR: 0.0152%
- gnomAD_E_NFE: 0.0036%
- gnomAD_E_SAS: 0.0033%
- Transcripts:
- HYDIN:ENST00000393567.2:c.7334A>T:p.(Asn2445Ile)
- Pathogenicity Data:
- Best Score: 0.68200004
- SIFT: 0.318 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.11518G>C:p.(Val3840Leu)
- Pathogenicity Data:
- Best Score: 0.64100003
- SIFT: 0.359 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.11606T>G:p.(Met3869Arg)
- Pathogenicity Data:
- Best Score: 0.61399996
- SIFT: 0.386 (T)
- Frequency Data:
- gnomAD_G_AFR: 0.0115%
- Transcripts:
- HYDIN:ENST00000393567.2:c.7588A>G:p.(Lys2530Glu)
- Pathogenicity Data:
- Best Score: 0.56700003
- SIFT: 0.433 (T)
- Frequency Data:
- TOPMed: 0.0004%
- Transcripts:
- HYDIN:ENST00000393567.2:c.11215G>A:p.(Ala3739Thr)
- Pathogenicity Data:
- Best Score: 0.528
- SIFT: 0.472 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.7766A>G:p.(Lys2589Arg)
- Pathogenicity Data:
- Best Score: 0.51
- SIFT: 0.490 (T)
- Frequency Data:
- TOPMed: 0.0008%
- Transcripts:
- HYDIN:ENST00000393567.2:c.7708G>A:p.(Asp2570Asn)
- Pathogenicity Data:
- Best Score: 0.464
- SIFT: 0.536 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.6295G>A:p.(Val2099Met)
- Pathogenicity Data:
- Best Score: 0.31199998
- SIFT: 0.688 (T)
- Frequency Data:
- TOPMed: 0.0032%
- Transcripts:
- HYDIN:ENST00000393567.2:c.7673G>A:p.(Gly2558Glu)
- Pathogenicity Data:
- Best Score: 0.18199998
- SIFT: 0.818 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.8081T>G:p.(Ile2694Ser)
- Pathogenicity Data:
- Best Score: 0.143
- SIFT: 0.857 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.7505T>C:p.(Leu2502Ser)
- Pathogenicity Data:
- Best Score: 0.10500002
- SIFT: 0.895 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.12076G>A:p.(Ala4026Thr)
- Pathogenicity Data:
- Best Score: 0.102999985
- SIFT: 0.897 (T)
- Frequency Data:
- gnomAD_G_AFR: 0.0129%
- gnomAD_G_NFE: 0.0068%
- Transcripts:
- HYDIN:ENST00000393567.2:c.12468A>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.11610T>C:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.10917C>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.10644T>C:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.10371C>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.8961G>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.7707A>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.7470G>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.6375C>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.4944A>G:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000288168.10:c.2049G>A:p.(=)
- HYDIN:ENST00000321489.5:c.1998G>A:p.(=)
- HYDIN:ENST00000393550.2:c.2043G>A:p.(=)
- HYDIN:ENST00000393567.2:c.1998G>A:p.(=)
- HYDIN:ENST00000448089.2:c.1998G>A:p.(=)
- HYDIN:ENST00000448691.1:c.1998G>A:p.(=)
- HYDIN:ENST00000538248.1:c.2079G>A:p.(=)
- HYDIN:ENST00000541601.1:c.2049G>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_SAS: 0.0033%
- Transcripts:
- HYDIN:ENST00000393567.2:c.12327T>C:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AMR: 0.0094%
- gnomAD_E_EAS: 0.0060%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_OTH: 0.0189%
- gnomAD_E_SAS: 0.0033%
- gnomAD_G_NFE: 0.0139%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_NFE: 0.0076%
- gnomAD_E_OTH: 0.0591%
- gnomAD_E_SAS: 0.0143%
- gnomAD_G_NFE: 0.0070%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0200%
- ExAC AFR: 0.1134%
- ExAC EAS: 0.0234%
- ExAC NFE: 0.0031%
- gnomAD_E_AFR: 0.0683%
- gnomAD_E_EAS: 0.0130%
- gnomAD_E_FIN: 0.0049%
- gnomAD_E_NFE: 0.0061%
- gnomAD_G_AFR: 0.0475%
- gnomAD_G_FIN: 0.0288%
- gnomAD_G_NFE: 0.0067%
- Transcripts:
- HYDIN:ENST00000393567.2:c.11100C>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.1179%
- gnomAD_E_AMR: 0.0060%
- gnomAD_G_AFR: 0.0803%
- Transcripts:
- HYDIN:ENST00000393567.2:c.3840G>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_FIN: 0.0046%
- gnomAD_E_NFE: 0.0054%
- gnomAD_G_AFR: 0.0508%
- gnomAD_G_AMR: 0.1330%
- gnomAD_G_EAS: 0.1439%
- gnomAD_G_NFE: 0.0437%
- Transcripts:
- HYDIN:ENST00000288168.10:c.1242G>A:p.(=)
- HYDIN:ENST00000321489.5:c.1191G>A:p.(=)
- HYDIN:ENST00000393550.2:c.1191G>A:p.(=)
- HYDIN:ENST00000393567.2:c.1191G>A:p.(=)
- HYDIN:ENST00000448089.2:c.1191G>A:p.(=)
- HYDIN:ENST00000448691.1:c.1191G>A:p.(=)
- HYDIN:ENST00000538248.1:c.1272G>A:p.(=)
- HYDIN:ENST00000541601.1:c.1242G>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AMR: 0.0186%
- gnomAD_E_EAS: 0.0060%
- gnomAD_E_FIN: 0.0092%
- gnomAD_E_NFE: 0.0083%
- gnomAD_E_OTH: 0.0191%
- gnomAD_E_SAS: 0.0138%
- gnomAD_G_AFR: 0.0991%
- gnomAD_G_EAS: 0.1418%
- gnomAD_G_NFE: 0.0508%
- gnomAD_G_OTH: 0.3326%
- Transcripts:
- HYDIN:ENST00000288168.10:c.1926A>G:p.(=)
- HYDIN:ENST00000321489.5:c.1875A>G:p.(=)
- HYDIN:ENST00000393550.2:c.1920A>G:p.(=)
- HYDIN:ENST00000393567.2:c.1875A>G:p.(=)
- HYDIN:ENST00000448089.2:c.1875A>G:p.(=)
- HYDIN:ENST00000448691.1:c.1875A>G:p.(=)
- HYDIN:ENST00000538248.1:c.1956A>G:p.(=)
- HYDIN:ENST00000541601.1:c.1926A>G:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_G_AFR: 0.3211%
- gnomAD_G_EAS: 0.4255%
- Pathogenicity Data:
- Best Score: 0.046000004
- SIFT: 0.954 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.9871G>C:p.(Ala3291Pro)
- Pathogenicity Data:
- Best Score: 0.0
- SIFT: 1.000 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.6827A>G:p.(Gln2276Arg)
- Pathogenicity Data:
- Best Score: 0.0
- SIFT: 1.000 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- HYDIN:ENST00000393567.2:c.6725A>G:p.(Gln2242Arg)
- Pathogenicity Data:
- Best Score: 0.0
- SIFT: 1.000 (T)
- Frequency Data:
- gnomAD_E_AFR: 0.2650%
- gnomAD_E_AMR: 0.3918%
- gnomAD_E_EAS: 0.7308%
- gnomAD_E_FIN: 0.0046%
- gnomAD_E_NFE: 0.1732%
- gnomAD_E_OTH: 0.3832%
- gnomAD_E_SAS: 0.2220%
- gnomAD_G_AFR: 0.0494%
- gnomAD_G_AMR: 0.1316%
- gnomAD_G_FIN: 0.0307%
- gnomAD_G_NFE: 0.0215%
- Phenotypic similarity 0.637 to mouse mutant involving PKD1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0003409, decreased width of hypertrophic chondrocyte zone
- HP:0001363, Craniosynostosis - MP:0003420, delayed intramembranous bone ossification
- HP:0011304, Broad thumb - MP:0003409, decreased width of hypertrophic chondrocyte zone
- HP:0010055, Broad hallux - MP:0003409, decreased width of hypertrophic chondrocyte zone
- Proximity score 0.508 in interactome to IFT88 and phenotypic similarity 0.814 to mouse mutant of IFT88.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000562, polydactyly
- HP:0001363, Craniosynostosis - MP:0003840, abnormal coronal suture morphology
- HP:0011304, Broad thumb - MP:0005306, abnormal phalanx morphology
- HP:0010055, Broad hallux - MP:0005104, abnormal tarsal bone morphology
- Known diseases:
- OMIM:173900 Polycystic kidney disease 1 - autosomal dominant
- ORPHA:730 Autosomal dominant polycystic kidney disease - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.925
Phenotype Score: 0.637
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 0.999999
- Polyphen2: 0.996 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.017 (D)
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.638 to Erythrokeratodermia variabilis associated with GJB4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001182, Tapered finger
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Proximity score 0.500 in interactome to GJB3 and phenotypic similarity 0.638 to Erythrokeratodermia variabilis associated with GJB3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001182, Tapered finger
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Known diseases:
- OMIM:617524 Erythrokeratodermia variabilis et progressiva 2 - autosomal dominant
- ORPHA:317 Erythrokeratodermia variabilis - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.923
Phenotype Score: 0.638
Variant Score: 0.996
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.638 to ORPHA:317 Erythrokeratodermia variabilis
- Phenotypic similarity 0.175 to OMIM:617524 Erythrokeratodermia variabilis et progressiva 2
- Transcripts:
- GJB4:ENST00000339480.1:c.673C>T:p.(Arg225Trp)
- Pathogenicity Data:
- Best Score: 0.997
- Polyphen2: 0.394 (B)
- SIFT: 0.003 (D)
- Frequency Data:
- TOPMed: 0.0004%
- ExAC SAS: 0.0061%
- gnomAD_E_NFE: 0.0018%
- gnomAD_E_SAS: 0.0032%
- Phenotypic similarity 0.570 to Kleefstra syndrome due to a point mutation associated with KMT2C.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001182, Tapered finger
- HP:0001363, Craniosynostosis - HP:0001357, Plagiocephaly
- HP:0011304, Broad thumb - HP:0001182, Tapered finger
- HP:0010055, Broad hallux - HP:0001182, Tapered finger
- Phenotypic similarity 0.268 to mouse mutant involving KMT2C.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001290, delayed eyelid opening
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.535 in interactome to KDM4B and phenotypic similarity 0.869 to Non-specific syndromic intellectual disability associated with KDM4B.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010109, Short hallux
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0011304, Broad thumb
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
- Known diseases:
- OMIM:617768 Kleefstra syndrome 2 - autosomal dominant
- ORPHA:261652 Kleefstra syndrome due to a point mutation - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.861
Phenotype Score: 0.570
Variant Score: 1.000
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.570 to ORPHA:261652 Kleefstra syndrome due to a point mutation
- Phenotypic similarity 0.426 to OMIM:617768 Kleefstra syndrome 2
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.210
Phenotype Score: 0.268
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.999989
- Polyphen2: 0.996 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.006 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.999337
- Polyphen2: 0.796 (P)
- Mutation Taster: 0.999 (P)
- SIFT: 0.001 (D)
- Frequency Data:
- TOPMed: 0.0004%
- Pathogenicity Data:
- Best Score: 0.994
- Polyphen2: 0.994 (D)
- Mutation Taster: 0.986 (P)
- SIFT: 0.023 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.977932
- Polyphen2: 0.131 (B)
- Mutation Taster: 0.978 (P)
- SIFT: 0.031 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.709 to Short-rib thoracic dysplasia 9 with or without polydactyly associated with IFT140.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0009803, Short phalanx of finger
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0009803, Short phalanx of finger
- HP:0010055, Broad hallux - HP:0009803, Short phalanx of finger
- Phenotypic similarity 0.737 to mouse mutant involving IFT140.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000562, polydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0000562, polydactyly
- HP:0010055, Broad hallux - MP:0000562, polydactyly
- Proximity score 0.524 in interactome to IFT43 and phenotypic similarity 0.729 to Cranioectodermal dysplasia associated with IFT43.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0009882, Short distal phalanx of finger
- HP:0010055, Broad hallux - HP:0008388, Abnormal toenail morphology
- Known diseases:
- OMIM:266920 Short-rib thoracic dysplasia 9 with or without polydactyly - autosomal recessive
- OMIM:617781 Retinitis pigmentosa 80 - autosomal recessive
- ORPHA:474 Jeune syndrome - autosomal recessive
- ORPHA:65 Leber congenital amaurosis - autosomal dominant/recessive
- ORPHA:791 Retinitis pigmentosa - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.848
Phenotype Score: 0.737
Variant Score: 0.800
- Transcripts:
- IFT140:ENST00000426508.2:c.1434G>C:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.737 to Intellectual disability-craniofacial dysmorphism-cryptorchidism syndrome associated with PACS1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001238, Slender finger
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0011304, Broad thumb
- HP:0010055, Broad hallux - HP:0001238, Slender finger
- Known diseases:
- OMIM:615009 Schuurs-Hoeijmakers syndrome - autosomal dominant
- ORPHA:329224 Intellectual disability-craniofacial dysmorphism-cryptorchidism syndrome - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.847
Phenotype Score: 0.737
Variant Score: 0.799
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.737 to ORPHA:329224 Intellectual disability-craniofacial dysmorphism-cryptorchidism syndrome
- Phenotypic similarity 0.352 to OMIM:615009 Schuurs-Hoeijmakers syndrome
- Transcripts:
- PACS1:ENST00000320580.4:c.661-5C>T:p.?
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_EAS: 0.0116%
- gnomAD_G_NFE: 0.0067%
- Phenotypic similarity 0.539 to Van Maldergem syndrome 1 associated with DCHS1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0030084, Clinodactyly
- HP:0001363, Craniosynostosis - HP:0010537, Wide cranial sutures
- HP:0011304, Broad thumb - HP:0010554, Cutaneous finger syndactyly
- HP:0010055, Broad hallux - HP:0030084, Clinodactyly
- Phenotypic similarity 0.555 to mouse mutant involving DCHS1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0012279, wide sternum
- HP:0001363, Craniosynostosis - MP:0008272, abnormal endochondral bone ossification
- HP:0011304, Broad thumb - MP:0012279, wide sternum
- HP:0010055, Broad hallux - MP:0012279, wide sternum
- Proximity score 0.501 in interactome to FAT4 and phenotypic similarity 0.739 to Hennekam syndrome associated with FAT4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0006101, Finger syndactyly
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0100490, Camptodactyly of finger
- HP:0010055, Broad hallux - HP:0006101, Finger syndactyly
- Proximity score 0.501 in interactome to FAT4 and phenotypic similarity 0.553 to mouse mutant of FAT4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0012279, wide sternum
- HP:0001363, Craniosynostosis - MP:0008272, abnormal endochondral bone ossification
- HP:0011304, Broad thumb - MP:0012279, wide sternum
- HP:0010055, Broad hallux - MP:0012279, wide sternum
- Known diseases:
- OMIM:601390 Van Maldergem syndrome 1 - autosomal recessive
- OMIM:607829 Mitral valve prolapse 2 - autosomal dominant
- ORPHA:314679 Cerebrofacioarticular syndrome - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.841
Phenotype Score: 0.555
Variant Score: 1.000
- Transcripts:
- DCHS1:ENST00000299441.3:c.8666G>C:p.(Arg2889Pro)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.968 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.018 (D)
- Frequency Data:
- No frequency data
- Proximity score 0.555 in interactome to GATAD2B and phenotypic similarity 0.745 to Severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome associated with GATAD2B.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010511, Long toe
- HP:0001363, Craniosynostosis - HP:0002007, Frontal bossing
- HP:0011304, Broad thumb - HP:0009836, Broad distal phalanx of finger
- HP:0010055, Broad hallux - HP:0010511, Long toe
- Proximity score 0.555 in interactome to GATAD2B and phenotypic similarity 0.252 to mouse mutant of GATAD2B.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0003795, abnormal bone structure
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.832
Phenotype Score: 0.555
Variant Score: 0.993
- Transcripts:
- CTBP2:ENST00000309035.6:c.2933A>G:p.(Asn978Ser)
- CTBP2:ENST00000334808.6:c.1517A>G:p.(Asn506Ser)
- CTBP2:ENST00000337195.5:c.1313A>G:p.(Asn438Ser)
- CTBP2:ENST00000411419.2:c.1313A>G:p.(Asn438Ser)
- CTBP2:ENST00000494626.2:c.1313A>G:p.(Asn438Ser)
- CTBP2:ENST00000531469.1:c.1313A>G:p.(Asn438Ser)
- Pathogenicity Data:
- Best Score: 0.994
- Polyphen2: 0.406 (B)
- SIFT: 0.006 (D)
- Frequency Data:
- gnomAD_E_EAS: 0.0058%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.076
Phenotype Score: 0.555
Variant Score: 0.547
- Transcripts:
- CTBP2:ENST00000309035.6:c.2933A>G:p.(Asn978Ser)
- CTBP2:ENST00000334808.6:c.1517A>G:p.(Asn506Ser)
- CTBP2:ENST00000337195.5:c.1313A>G:p.(Asn438Ser)
- CTBP2:ENST00000411419.2:c.1313A>G:p.(Asn438Ser)
- CTBP2:ENST00000494626.2:c.1313A>G:p.(Asn438Ser)
- CTBP2:ENST00000531469.1:c.1313A>G:p.(Asn438Ser)
- Pathogenicity Data:
- Best Score: 0.994
- Polyphen2: 0.406 (B)
- SIFT: 0.006 (D)
- Frequency Data:
- gnomAD_E_EAS: 0.0058%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.712 to Trichothiodystrophy associated with RNF113A.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001217, Clubbing
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0001217, Clubbing
- HP:0010055, Broad hallux - HP:0001217, Clubbing
- Phenotypic similarity 0.262 to mouse mutant involving RNF113A.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0002792, abnormal retinal vasculature morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.500 in interactome to SNIP1 and phenotypic similarity 0.761 to Psychomotor retardation, epilepsy, and craniofacial dysmorphism associated with SNIP1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001182, Tapered finger
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0011304, Broad thumb
- HP:0010055, Broad hallux - HP:0001182, Tapered finger
- Proximity score 0.500 in interactome to SNIP1 and phenotypic similarity 0.262 to mouse mutant of SNIP1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0006241, abnormal placement of pupils
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Known diseases:
- OMIM:300953 Trichothiodystrophy 5, nonphotosensitive - X-linked dominant
- ORPHA:33364 Trichothiodystrophy - X-linked dominant
X_DOMINANT
Exomiser Score: 0.823
Phenotype Score: 0.712
Variant Score: 0.809
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.712 to ORPHA:33364 Trichothiodystrophy
- Transcripts:
- RNF113A:ENST00000371442.2:c.266A>G:p.(Glu89Gly)
- Pathogenicity Data:
- Best Score: 0.809
- Polyphen2: 0.002 (B)
- SIFT: 0.191 (T)
- Frequency Data:
- TOPMed: 0.0008%
X_RECESSIVE
Exomiser Score: 0.037
Phenotype Score: 0.250
Variant Score: 0.809
- Transcripts:
- RNF113A:ENST00000371442.2:c.266A>G:p.(Glu89Gly)
- Pathogenicity Data:
- Best Score: 0.809
- Polyphen2: 0.002 (B)
- SIFT: 0.191 (T)
- Frequency Data:
- TOPMed: 0.0008%
- Phenotypic similarity 0.384 to mouse mutant involving TDG.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0006279, abnormal limb development
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0006279, abnormal limb development
- HP:0010055, Broad hallux - MP:0006279, abnormal limb development
- Proximity score 0.536 in interactome to MBD4 and phenotypic similarity 0.772 to mouse mutant of MBD4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0004083, polysyndactyly
- HP:0001363, Craniosynostosis - MP:0001286, abnormal eye development
- HP:0011304, Broad thumb - MP:0005230, ectrodactyly
- HP:0010055, Broad hallux - MP:0005230, ectrodactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.812
Phenotype Score: 0.536
Variant Score: 1.000
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.806
Phenotype Score: 0.536
Variant Score: 0.995
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0067%
- gnomAD_E_AMR: 0.0032%
- gnomAD_E_FIN: 0.0232%
- gnomAD_E_NFE: 0.0224%
- gnomAD_E_OTH: 0.0194%
- gnomAD_E_SAS: 0.0645%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0799%
- TOPMed: 0.0799%
- ExAC EAS: 0.1387%
- gnomAD_E_EAS: 0.1276%
- gnomAD_G_EAS: 0.3083%
- Proximity score 0.534 in interactome to ALX4 and phenotypic similarity 0.839 to Enlarged parietal foramina associated with ALX4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0011304, Broad thumb
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0011304, Broad thumb
- HP:0010055, Broad hallux - HP:0011304, Broad thumb
- Proximity score 0.534 in interactome to ALX4 and phenotypic similarity 0.775 to mouse mutant of ALX4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000562, polydactyly
- HP:0001363, Craniosynostosis - MP:0000109, abnormal parietal bone morphology
- HP:0011304, Broad thumb - MP:0000562, polydactyly
- HP:0010055, Broad hallux - MP:0000562, polydactyly
- Known diseases:
- OMIM:617039 Patent ductus arteriosus 3 - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.809
Phenotype Score: 0.534
Variant Score: 1.000
- Transcripts:
- PRDM6:ENST00000407847.4:c.1133G>A:p.(Cys378Tyr)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.737 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.079 (T)
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.334 to Autosomal dominant hypohidrotic ectodermal dysplasia associated with TRAF6.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001231, Abnormal fingernail morphology
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001231, Abnormal fingernail morphology
- HP:0010055, Broad hallux - HP:0001231, Abnormal fingernail morphology
- Phenotypic similarity 0.533 to mouse mutant involving TRAF6.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000133, abnormal long bone metaphysis morphology
- HP:0001363, Craniosynostosis - MP:0000062, increased bone mineral density
- HP:0011304, Broad thumb - MP:0000133, abnormal long bone metaphysis morphology
- HP:0010055, Broad hallux - MP:0000133, abnormal long bone metaphysis morphology
- Proximity score 0.533 in interactome to DYNC2I2 and phenotypic similarity 0.662 to Jeune syndrome associated with DYNC2I2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001162, Postaxial hand polydactyly
- HP:0010055, Broad hallux - HP:0001770, Toe syndactyly
- Proximity score 0.533 in interactome to DYNC2I2 and phenotypic similarity 0.699 to mouse mutant of DYNC2I2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000562, polydactyly
- HP:0001363, Craniosynostosis - MP:0001297, microphthalmia
- HP:0011304, Broad thumb - MP:0000562, polydactyly
- HP:0010055, Broad hallux - MP:0000562, polydactyly
- Known diseases:
- ORPHA:1810 Autosomal dominant hypohidrotic ectodermal dysplasia - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.805
Phenotype Score: 0.533
Variant Score: 0.998
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.334 to ORPHA:1810 Autosomal dominant hypohidrotic ectodermal dysplasia
- Pathogenicity Data:
- Best Score: 0.999982
- Polyphen2: 0.831 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.004 (D)
- Frequency Data:
- TOPMed: 0.0004%
- gnomAD_G_AFR: 0.0115%
- Proximity score 0.520 in interactome to MAP3K20 and phenotypic similarity 0.382 to Split-foot malformation with mesoaxial polydactyly associated with MAP3K20.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0012725, Cutaneous syndactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0012725, Cutaneous syndactyly
- HP:0010055, Broad hallux - HP:0012725, Cutaneous syndactyly
- Proximity score 0.520 in interactome to MAP3K20 and phenotypic similarity 0.723 to mouse mutant of MAP3K20.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000562, polydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0000562, polydactyly
- HP:0010055, Broad hallux - MP:0000562, polydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.785
Phenotype Score: 0.520
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.986 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.129 (T)
- Frequency Data:
- gnomAD_E_NFE: 0.0022%
- Phenotypic similarity 0.629 to mouse mutant involving PRKRA.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0030029, wide cranial sutures
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.500 in interactome to TNRC6B and phenotypic similarity 0.869 to Non-specific syndromic intellectual disability associated with TNRC6B.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010109, Short hallux
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0011304, Broad thumb
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
- Known diseases:
- OMIM:612067 Dystonia 16 - autosomal recessive
- ORPHA:210571 Dystonia 16 - autosomal recessive
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.778
Phenotype Score: 0.629
Variant Score: 0.871
- Pathogenicity Data:
- Best Score: 0.999994
- Polyphen2: 0.936 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.002 (D)
- Frequency Data:
- gnomAD_E_EAS: 0.0058%
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.993 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.008 (D)
- Frequency Data:
- gnomAD_E_AFR: 0.2121%
- gnomAD_E_AMR: 1.0638%
- gnomAD_E_EAS: 0.5170%
- gnomAD_E_FIN: 0.3058%
- gnomAD_E_NFE: 0.5882%
- gnomAD_E_OTH: 0.6875%
- gnomAD_E_SAS: 0.5048%
AUTOSOMAL_DOMINANT
Exomiser Score: 0.301
Phenotype Score: 0.315
Variant Score: 0.999
- Pathogenicity Data:
- Best Score: 0.999994
- Polyphen2: 0.936 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.002 (D)
- Frequency Data:
- gnomAD_E_EAS: 0.0058%
- Phenotypic similarity 0.340 to Immunodeficiency 10 associated with STIM1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0002164, Nail dysplasia
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0002164, Nail dysplasia
- HP:0010055, Broad hallux - HP:0002164, Nail dysplasia
- Phenotypic similarity 0.320 to mouse mutant involving STIM1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0002092, abnormal eye morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.513 in interactome to ASPH and phenotypic similarity 0.737 to mouse mutant of ASPH.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000564, syndactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0000564, syndactyly
- HP:0010055, Broad hallux - MP:0000564, syndactyly
- Known diseases:
- OMIM:160565 Myopathy, tubular aggregate, 1 - autosomal dominant
- OMIM:185070 Stormorken syndrome - autosomal dominant
- OMIM:612783 Immunodeficiency 10 - autosomal recessive
- ORPHA:2593 Tubular aggregate myopathy - autosomal dominant
- ORPHA:3204 Stormorken-Sjaastad-Langslet syndrome - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.773
Phenotype Score: 0.513
Variant Score: 1.000
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.158 to OMIM:160565 Myopathy, tubular aggregate, 1
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.843 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- ExAC NFE: 0.0015%
- gnomAD_E_NFE: 0.0009%
- Proximity score 0.508 in interactome to APC2 and phenotypic similarity 0.717 to Sotos syndrome associated with APC2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0004691, 2-3 toe syndactyly
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0005617, Bilateral camptodactyly
- HP:0010055, Broad hallux - HP:0004691, 2-3 toe syndactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.764
Phenotype Score: 0.508
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.521 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.055 (D)
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.764
Phenotype Score: 0.508
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.521 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.055 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.004 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.647 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.101 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.009 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.931 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.895 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.455 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.007 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.992 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.005 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.998 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.001 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.003 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.127 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- CDC27:ENST00000066544.3:c.1071-3_1071-2insCTGTCTTCTCGCAGAGGGGAAAGAGCCGAAAGGTAACTCCAGTCCTTGCAAAAACACAA:p.?
- CDC27:ENST00000446365.2:c.888-3_888-2insCTGTCTTCTCGCAGAGGGGAAAGAGCCGAAAGGTAACTCCAGTCCTTGCAAAAACACAA:p.?
- CDC27:ENST00000527547.1:c.1071-3_1071-2insCTGTCTTCTCGCAGAGGGGAAAGAGCCGAAAGGTAACTCCAGTCCTTGCAAAAACACAA:p.?
- CDC27:ENST00000531206.1:c.1089-3_1089-2insCTGTCTTCTCGCAGAGGGGAAAGAGCCGAAAGGTAACTCCAGTCCTTGCAAAAACACAA:p.?
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.540 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.042 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.002 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.261 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.758 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.083 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.942 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.999999
- Polyphen2: 0.991 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.001 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.999998
- Polyphen2: 0.995 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.004 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.999998
- Mutation Taster: 1.000 (P)
- SIFT: 0.084 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.999998
- Polyphen2: 0.101 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.007 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.999997
- Polyphen2: 0.005 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.338 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.999996
- Polyphen2: 0.007 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.447 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.999996
- Polyphen2: 0.001 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.694 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.999994
- Polyphen2: 0.079 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.007 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.99999
- Polyphen2: 0.004 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.304 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.999982
- Polyphen2: 0.093 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.100 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.999962
- Polyphen2: 0.548 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.050 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.99982
- Polyphen2: 0.002 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.456 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.999577
- Polyphen2: 0.082 (B)
- Mutation Taster: 1.000 (P)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.998578
- Polyphen2: 0.006 (B)
- Mutation Taster: 0.999 (P)
- SIFT: 0.128 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.997774
- Polyphen2: 0.001 (B)
- Mutation Taster: 0.998 (P)
- SIFT: 0.139 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.667 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.065 (T)
- Frequency Data:
- gnomAD_E_FIN: 0.0091%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_OTH: 0.0185%
- gnomAD_E_SAS: 0.0067%
- Pathogenicity Data:
- Best Score: 0.999994
- Polyphen2: 0.341 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.012 (D)
- Frequency Data:
- gnomAD_E_OTH: 0.0190%
- gnomAD_E_SAS: 0.0034%
- Pathogenicity Data:
- Best Score: 0.999974
- Polyphen2: 0.158 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.017 (D)
- Frequency Data:
- gnomAD_E_OTH: 0.0190%
- Pathogenicity Data:
- Best Score: 0.996494
- Polyphen2: 0.001 (B)
- Mutation Taster: 0.996 (P)
- SIFT: 0.271 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.878 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.019 (D)
- Frequency Data:
- gnomAD_E_AFR: 0.0138%
- gnomAD_E_AMR: 0.0553%
- gnomAD_E_EAS: 0.0502%
- gnomAD_E_FIN: 0.0185%
- gnomAD_E_NFE: 0.0111%
- gnomAD_E_OTH: 0.0386%
- gnomAD_E_SAS: 0.0034%
- Pathogenicity Data:
- Best Score: 0.959
- Polyphen2: 0.002 (B)
- Mutation Taster: 0.832
- SIFT: 0.041 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.895 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- gnomAD_E_AFR: 0.0087%
- gnomAD_E_AMR: 0.2800%
- gnomAD_E_EAS: 0.0621%
- gnomAD_E_FIN: 0.0330%
- gnomAD_E_NFE: 0.0523%
- gnomAD_E_OTH: 0.0248%
- gnomAD_E_SAS: 0.2146%
- gnomAD_G_FIN: 0.0911%
- Pathogenicity Data:
- Best Score: 0.954154
- Polyphen2: 0.004 (B)
- Mutation Taster: 0.954 (P)
- SIFT: 0.056 (D)
- Frequency Data:
- ExAC FIN: 0.0151%
- gnomAD_E_FIN: 0.0045%
- Pathogenicity Data:
- Best Score: 0.999906
- Polyphen2: 0.011 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.077 (T)
- Frequency Data:
- gnomAD_E_AFR: 0.0181%
- gnomAD_E_AMR: 0.4336%
- gnomAD_E_EAS: 0.0681%
- gnomAD_E_FIN: 0.0430%
- gnomAD_E_NFE: 0.0791%
- gnomAD_E_OTH: 0.2074%
- gnomAD_E_SAS: 0.3257%
- gnomAD_G_FIN: 0.0605%
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.010 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.099 (T)
- Frequency Data:
- gnomAD_E_AFR: 0.0469%
- gnomAD_E_AMR: 0.4822%
- gnomAD_E_EAS: 0.2092%
- gnomAD_E_FIN: 0.1639%
- gnomAD_E_NFE: 0.1398%
- gnomAD_E_OTH: 0.2127%
- gnomAD_E_SAS: 0.4125%
- gnomAD_G_AFR: 0.0241%
- gnomAD_G_FIN: 0.0314%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- CDC27:ENST00000066544.3:c.1071_1072insTCTGGTCCGCCGACA:p.(Ser357_Thr358insSerGlyProProThr)
- CDC27:ENST00000446365.2:c.888_889insTCTGGTCCGCCGACA:p.(Ser296_Thr297insSerGlyProProThr)
- CDC27:ENST00000527547.1:c.1071_1072insTCTGGTCCGCCGACA:p.(Ser357_Thr358insSerGlyProProThr)
- CDC27:ENST00000531206.1:c.1089_1090insTCTGGTCCGCCGACA:p.(Ser363_Thr364insSerGlyProProThr)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC NFE: 0.0017%
- Pathogenicity Data:
- Best Score: 0.66499996
- Polyphen2: 0.001 (B)
- SIFT: 0.335 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.458
- SIFT: 0.542 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.144
- SIFT: 0.856 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC NFE: 0.0016%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_SAS: 0.0033%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC SAS: 0.0061%
- gnomAD_E_SAS: 0.0033%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC SAS: 0.0078%
- gnomAD_E_NFE: 0.0010%
- gnomAD_E_SAS: 0.0039%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0067%
- gnomAD_E_AMR: 0.0093%
- gnomAD_E_EAS: 0.0061%
- gnomAD_E_NFE: 0.0018%
- gnomAD_E_SAS: 0.0066%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC AMR: 0.0139%
- gnomAD_E_SAS: 0.0034%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_OTH: 0.0184%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0070%
- gnomAD_E_AMR: 0.0033%
- gnomAD_E_FIN: 0.0245%
- gnomAD_E_NFE: 0.0173%
- gnomAD_E_OTH: 0.0198%
- gnomAD_E_SAS: 0.0036%
- gnomAD_G_NFE: 0.0136%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0011%
- ExAC NFE: 0.0045%
- ExAC SAS: 0.0061%
- gnomAD_E_NFE: 0.0027%
- gnomAD_E_OTH: 0.0379%
- gnomAD_E_SAS: 0.0171%
- gnomAD_G_NFE: 0.0067%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AMR: 0.0031%
- gnomAD_G_EAS: 0.0617%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0091%
- ExAC EAS: 0.1736%
- ExAC OTH: 0.1104%
- gnomAD_E_EAS: 0.1451%
- gnomAD_E_NFE: 0.0009%
- gnomAD_G_EAS: 0.0617%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0200%
- gnomAD_E_AFR: 0.0088%
- gnomAD_E_AMR: 0.2838%
- gnomAD_E_EAS: 0.0362%
- gnomAD_E_FIN: 0.0236%
- gnomAD_E_NFE: 0.0570%
- gnomAD_E_SAS: 0.2353%
- gnomAD_G_AFR: 0.0115%
- gnomAD_G_FIN: 0.0918%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.3692%
- gnomAD_E_AMR: 0.9489%
- gnomAD_E_EAS: 0.3497%
- gnomAD_E_FIN: 0.6602%
- gnomAD_E_NFE: 0.3351%
- gnomAD_E_OTH: 0.5086%
- gnomAD_E_SAS: 0.7459%
- gnomAD_G_AFR: 0.0118%
- gnomAD_G_NFE: 0.0143%
- Proximity score 0.517 in interactome to HS2ST1 and phenotypic similarity 0.703 to Neurofacioskeletal syndrome with or without renal agenesis associated with HS2ST1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0011927, Short digit
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009836, Broad distal phalanx of finger
- HP:0010055, Broad hallux - HP:0010186, Broad distal phalanx of the toes
- Proximity score 0.517 in interactome to HS2ST1 and phenotypic similarity 0.698 to mouse mutant of HS2ST1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000562, polydactyly
- HP:0001363, Craniosynostosis - MP:0002896, abnormal bone mineralization
- HP:0011304, Broad thumb - MP:0000562, polydactyly
- HP:0010055, Broad hallux - MP:0000562, polydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.763
Phenotype Score: 0.517
Variant Score: 0.989
- Transcripts:
- HS6ST3:ENST00000376705.2:c.242G>T:p.(Gly81Val)
- Pathogenicity Data:
- Best Score: 0.989
- Polyphen2: 0.017 (B)
- SIFT: 0.011 (D)
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.052
Phenotype Score: 0.517
Variant Score: 0.545
- Transcripts:
- HS6ST3:ENST00000376705.2:c.242G>T:p.(Gly81Val)
- Pathogenicity Data:
- Best Score: 0.989
- Polyphen2: 0.017 (B)
- SIFT: 0.011 (D)
- Frequency Data:
- No frequency data
- Transcripts:
- HS6ST3:ENST00000376705.2:c.243A>C:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.507 in interactome to PLOD2 and phenotypic similarity 0.617 to Bruck syndrome 2 associated with PLOD2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0002980, Femoral bowing
- HP:0001363, Craniosynostosis - HP:0002645, Wormian bones
- HP:0011304, Broad thumb - HP:0002980, Femoral bowing
- HP:0010055, Broad hallux - HP:0002980, Femoral bowing
- Proximity score 0.507 in interactome to PLOD2 and phenotypic similarity 0.265 to mouse mutant of PLOD2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0005544, corneal deposits
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.507 in interactome to PLOD2 and phenotypic similarity 0.433 to fish mutant of PLOD2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - ZP:0006781, bone mineralization increased process quality, abnormal
- HP:0011304, Broad thumb - ZP:0020434, rib curved, abnormal
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.762
Phenotype Score: 0.507
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.999 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.014 (D)
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.762
Phenotype Score: 0.507
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.999 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.014 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.999998
- Polyphen2: 0.030 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.016 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.007 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.352 (T)
- Frequency Data:
- ExAC NFE: 0.0015%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0952%
- gnomAD_G_AFR: 0.0459%
- gnomAD_G_NFE: 0.0268%
- gnomAD_G_OTH: 0.1020%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.5192%
- TOPMed: 0.0291%
- gnomAD_E_AFR: 0.0070%
- gnomAD_E_AMR: 0.1789%
- gnomAD_E_NFE: 0.0037%
- gnomAD_G_AFR: 0.0229%
- gnomAD_G_AMR: 0.2387%
- Phenotypic similarity 0.327 to mouse mutant involving PER2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0020039, increased bone ossification
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.508 in interactome to NONO and phenotypic similarity 0.699 to Intellectual developmental disorder, X-linked syndromic 34 associated with NONO.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001822, Hallux valgus
- HP:0001363, Craniosynostosis - HP:0002684, Thickened calvaria
- HP:0011304, Broad thumb - HP:0001822, Hallux valgus
- HP:0010055, Broad hallux - HP:0001822, Hallux valgus
- Known diseases:
- OMIM:604348 ?Advanced sleep phase syndrome, familial, 1 (unconfirmed)
AUTOSOMAL_DOMINANT
Exomiser Score: 0.761
Phenotype Score: 0.508
Variant Score: 0.998
- Pathogenicity Data:
- Best Score: 0.998143
- Polyphen2: 0.074 (B)
- Mutation Taster: 0.998 (P)
- SIFT: 0.387 (T)
- Frequency Data:
- TOPMed: 0.0015%
- Proximity score 0.505 in interactome to APBB1IP and phenotypic similarity 0.755 to mouse mutant of APBB1IP.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.759
Phenotype Score: 0.505
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.968 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.006 (D)
- Frequency Data:
- TOPMed: 0.0008%
- Phenotypic similarity 0.175 to Familial isolated dilated cardiomyopathy associated with TNNI3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0000982, Palmoplantar keratoderma
- HP:0010055, Broad hallux - HP:0000982, Palmoplantar keratoderma
- Proximity score 0.504 in interactome to TNNI2 and phenotypic similarity 0.494 to Distal arthrogryposis type 1 associated with TNNI2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010557, Overlapping fingers
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001181, Adducted thumb
- HP:0010055, Broad hallux - HP:0010557, Overlapping fingers
- Proximity score 0.504 in interactome to TNNI2 and phenotypic similarity 0.611 to mouse mutant of TNNI2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0006395, abnormal epiphyseal plate morphology
- HP:0001363, Craniosynostosis - MP:0008273, abnormal intramembranous bone ossification
- HP:0011304, Broad thumb - MP:0004351, short humerus
- HP:0010055, Broad hallux - MP:0006395, abnormal epiphyseal plate morphology
- Known diseases:
- OMIM:115210 Cardiomyopathy, familial restrictive, 1 - autosomal dominant
- OMIM:611880 ?Cardiomyopathy, dilated, 2A (unconfirmed)
- OMIM:613286 Cardiomyopathy, dilated, 1FF - unknown
- OMIM:613690 Cardiomyopathy, hypertrophic, 7 - autosomal dominant
- ORPHA:154 Familial isolated dilated cardiomyopathy - autosomal recessive
- ORPHA:154 Familial isolated dilated cardiomyopathy - autosomal dominant/recessive
- ORPHA:75249 Familial isolated restrictive cardiomyopathy - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.757
Phenotype Score: 0.504
Variant Score: 1.000
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.175 to ORPHA:154 Familial isolated dilated cardiomyopathy
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.306 to mouse mutant involving FOXD4L5.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0002092, abnormal eye morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.504 in interactome to TFAP2A and phenotypic similarity 0.595 to Branchiooculofacial syndrome associated with TFAP2A.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0009778, Short thumb
- HP:0001363, Craniosynostosis - HP:0000268, Dolichocephaly
- HP:0011304, Broad thumb - HP:0001177, Preaxial hand polydactyly
- HP:0010055, Broad hallux - HP:0004209, Clinodactyly of the 5th finger
- Proximity score 0.504 in interactome to TFAP2A and phenotypic similarity 0.737 to mouse mutant of TFAP2A.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000562, polydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0000562, polydactyly
- HP:0010055, Broad hallux - MP:0000562, polydactyly
- Proximity score 0.504 in interactome to TFAP2A and phenotypic similarity 0.330 to fish mutant of TFAP2A.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - ZP:0001979, ethmoid cartilage split, abnormal
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.757
Phenotype Score: 0.504
Variant Score: 1.000
- Transcripts:
- FOXD4L5:ENST00000377420.1:c.514G>A:p.(Glu172Lys)
- Pathogenicity Data:
- Best Score: 0.999993
- Polyphen2: 0.955 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.015 (D)
- Frequency Data:
- No frequency data
- Proximity score 0.516 in interactome to CHST11 and phenotypic similarity 0.832 to ?Osteochondrodysplasia, brachydactyly, and overlapping malformed digits associated with CHST11.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009778, Short thumb
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
- Proximity score 0.516 in interactome to CHST11 and phenotypic similarity 0.716 to mouse mutant of CHST11.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0005306, abnormal phalanx morphology
- HP:0001363, Craniosynostosis - MP:0000440, domed cranium
- HP:0011304, Broad thumb - MP:0005306, abnormal phalanx morphology
- HP:0010055, Broad hallux - MP:0005109, abnormal talus morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.757
Phenotype Score: 0.516
Variant Score: 0.986
- Pathogenicity Data:
- Best Score: 0.989374
- Polyphen2: 0.889 (P)
- Mutation Taster: 0.989 (P)
- SIFT: 0.108 (T)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0008%
- ExAC AFR: 0.0192%
- ExAC EAS: 0.0231%
- gnomAD_E_AFR: 0.0131%
- gnomAD_E_EAS: 0.0058%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_SAS: 0.0065%
- Proximity score 0.504 in interactome to UBE4B and phenotypic similarity 0.667 to 1p36 deletion syndrome associated with UBE4B.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0000270, Delayed cranial suture closure
- HP:0011304, Broad thumb - HP:0100490, Camptodactyly of finger
- HP:0010055, Broad hallux - HP:0001829, Foot polydactyly
- Known diseases:
- OMIM:109150 Machado-Joseph disease - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.756
Phenotype Score: 0.504
Variant Score: 1.000
- Transcripts:
- ATXN3:ENST00000340660.6:c.750_751insCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA:p.(Gly251Glnfs*39)
- ATXN3:ENST00000393287.5:c.915_916insCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA:p.(Gly306Glnfs*39)
- ATXN3:ENST00000429774.2:c.894_895insCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA:p.(Gly299Glnfs*39)
- ATXN3:ENST00000502250.1:c.378_379insCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA:p.(Gly127Glnfs*39)
- ATXN3:ENST00000503767.1:c.870_871insCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA:p.(Gly291Glnfs*39)
- ATXN3:ENST00000532032.1:c.915_916insCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA:p.(Gly306Glnfs*39)
- ATXN3:ENST00000545170.1:c.942_943insCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA:p.(Gly315Glnfs*39)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.530 to Neurodevelopmental disorder with brain anomalies and with or without vertebral or cardiac anomalies associated with DHX37.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001792, Small nail
- HP:0001363, Craniosynostosis - HP:0001357, Plagiocephaly
- HP:0011304, Broad thumb - HP:0001792, Small nail
- HP:0010055, Broad hallux - HP:0001792, Small nail
- Proximity score 0.505 in interactome to DMP1 and phenotypic similarity 0.697 to Autosomal recessive hypophosphatemic rickets associated with DMP1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0002970, Genu varum
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0002982, Tibial bowing
- HP:0010055, Broad hallux - HP:0002970, Genu varum
- Proximity score 0.505 in interactome to DMP1 and phenotypic similarity 0.590 to mouse mutant of DMP1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000133, abnormal long bone metaphysis morphology
- HP:0001363, Craniosynostosis - MP:0000060, delayed bone ossification
- HP:0011304, Broad thumb - MP:0000133, abnormal long bone metaphysis morphology
- HP:0010055, Broad hallux - MP:0000133, abnormal long bone metaphysis morphology
- Known diseases:
- OMIM:273250 46, XY sex reversal 11 - autosomal dominant
- OMIM:618731 Neurodevelopmental disorder with brain anomalies and with or without vertebral or cardiac anomalies - autosomal recessive
- ORPHA:242 46,XY complete gonadal dysgenesis - autosomal dominant/recessive
- ORPHA:251510 46,XY partial gonadal dysgenesis - autosomal dominant/recessive
- ORPHA:983 Testicular regression syndrome - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.756
Phenotype Score: 0.505
Variant Score: 0.998
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.430 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.020 (D)
- Frequency Data:
- TOPMed: 0.0008%
- gnomAD_G_AFR: 0.0115%
- Proximity score 0.503 in interactome to PRICKLE1 and phenotypic similarity 0.870 to mouse mutant of PRICKLE1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002544, brachydactyly
- HP:0001363, Craniosynostosis - MP:0030049, prominent forehead
- HP:0011304, Broad thumb - MP:0002544, brachydactyly
- HP:0010055, Broad hallux - MP:0002544, brachydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.755
Phenotype Score: 0.503
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.943 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.045 (D)
- Frequency Data:
- TOPMed: 0.0004%
- Phenotypic similarity 0.498 to mouse mutant involving GGT1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0006396, decreased long bone epiphyseal plate size
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0003109, short femur
- HP:0010055, Broad hallux - MP:0003109, short femur
- Proximity score 0.506 in interactome to PCYT1A and phenotypic similarity 0.624 to Spondylometaphyseal dysplasia with cone-rod dystrophy associated with PCYT1A.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0010049, Short metacarpal
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Known diseases:
- OMIM:231950 ?Glutathioninuria (unconfirmed)
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.755
Phenotype Score: 0.506
Variant Score: 0.996
- Transcripts:
- GGT1:ENST00000248923.4:c.1361G>T:p.(Cys454Phe)
- GGT1:ENST00000400380.1:c.1361G>T:p.(Cys454Phe)
- GGT1:ENST00000400382.1:c.1361G>T:p.(Cys454Phe)
- GGT1:ENST00000400383.1:c.1361G>T:p.(Cys454Phe)
- GGT1:ENST00000401885.1:c.329G>T:p.(Cys110Phe)
- GGT1:ENST00000403838.1:c.329G>T:p.(Cys110Phe)
- GGT1:ENST00000404223.1:c.329G>T:p.(Cys110Phe)
- GGT1:ENST00000404532.1:c.329G>T:p.(Cys110Phe)
- GGT1:ENST00000404920.1:c.329G>T:p.(Cys110Phe)
- GGT1:ENST00000406383.2:c.1361G>T:p.(Cys454Phe)
- Pathogenicity Data:
- Best Score: 0.999907
- Polyphen2: 0.031 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.002 (D)
- Frequency Data:
- No frequency data
- Transcripts:
- GGT1:ENST00000248923.4:c.1063C>T:p.(Arg355Trp)
- GGT1:ENST00000400380.1:c.1063C>T:p.(Arg355Trp)
- GGT1:ENST00000400382.1:c.1063C>T:p.(Arg355Trp)
- GGT1:ENST00000400383.1:c.1063C>T:p.(Arg355Trp)
- GGT1:ENST00000401885.1:c.31C>T:p.(Arg11Trp)
- GGT1:ENST00000403838.1:c.31C>T:p.(Arg11Trp)
- GGT1:ENST00000404223.1:c.31C>T:p.(Arg11Trp)
- GGT1:ENST00000404532.1:c.31C>T:p.(Arg11Trp)
- GGT1:ENST00000404920.1:c.31C>T:p.(Arg11Trp)
- GGT1:ENST00000406383.2:c.1063C>T:p.(Arg355Trp)
- Pathogenicity Data:
- Best Score: 0.993
- Polyphen2: 0.716 (P)
- Mutation Taster: 0.945 (P)
- SIFT: 0.007 (D)
- Frequency Data:
- TOPMed: 0.0008%
- gnomAD_E_EAS: 0.0058%
- gnomAD_E_SAS: 0.0065%
AUTOSOMAL_DOMINANT
Exomiser Score: 0.186
Phenotype Score: 0.253
Variant Score: 1.000
- Transcripts:
- GGT1:ENST00000248923.4:c.1361G>T:p.(Cys454Phe)
- GGT1:ENST00000400380.1:c.1361G>T:p.(Cys454Phe)
- GGT1:ENST00000400382.1:c.1361G>T:p.(Cys454Phe)
- GGT1:ENST00000400383.1:c.1361G>T:p.(Cys454Phe)
- GGT1:ENST00000401885.1:c.329G>T:p.(Cys110Phe)
- GGT1:ENST00000403838.1:c.329G>T:p.(Cys110Phe)
- GGT1:ENST00000404223.1:c.329G>T:p.(Cys110Phe)
- GGT1:ENST00000404532.1:c.329G>T:p.(Cys110Phe)
- GGT1:ENST00000404920.1:c.329G>T:p.(Cys110Phe)
- GGT1:ENST00000406383.2:c.1361G>T:p.(Cys454Phe)
- Pathogenicity Data:
- Best Score: 0.999907
- Polyphen2: 0.031 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.002 (D)
- Frequency Data:
- No frequency data
- Transcripts:
- GGT1:ENST00000248923.4:c.1162G>A:p.(Ala388Thr)
- GGT1:ENST00000400380.1:c.1162G>A:p.(Ala388Thr)
- GGT1:ENST00000400382.1:c.1162G>A:p.(Ala388Thr)
- GGT1:ENST00000400383.1:c.1162G>A:p.(Ala388Thr)
- GGT1:ENST00000401885.1:c.130G>A:p.(Ala44Thr)
- GGT1:ENST00000403838.1:c.130G>A:p.(Ala44Thr)
- GGT1:ENST00000404223.1:c.130G>A:p.(Ala44Thr)
- GGT1:ENST00000404532.1:c.130G>A:p.(Ala44Thr)
- GGT1:ENST00000404920.1:c.130G>A:p.(Ala44Thr)
- GGT1:ENST00000406383.2:c.1162G>A:p.(Ala388Thr)
- Pathogenicity Data:
- Best Score: 0.968
- Polyphen2: 0.103 (B)
- Mutation Taster: 0.881
- SIFT: 0.032 (D)
- Frequency Data:
- TOPMed: 0.0008%
- gnomAD_E_AFR: 0.0083%
- gnomAD_E_AMR: 0.0032%
- gnomAD_E_NFE: 0.0021%
- gnomAD_E_SAS: 0.0035%
- Transcripts:
- GGT1:ENST00000248923.4:c.1135G>A:p.(Gly379Arg)
- GGT1:ENST00000400380.1:c.1135G>A:p.(Gly379Arg)
- GGT1:ENST00000400382.1:c.1135G>A:p.(Gly379Arg)
- GGT1:ENST00000400383.1:c.1135G>A:p.(Gly379Arg)
- GGT1:ENST00000401885.1:c.103G>A:p.(Gly35Arg)
- GGT1:ENST00000403838.1:c.103G>A:p.(Gly35Arg)
- GGT1:ENST00000404223.1:c.103G>A:p.(Gly35Arg)
- GGT1:ENST00000404532.1:c.103G>A:p.(Gly35Arg)
- GGT1:ENST00000404920.1:c.103G>A:p.(Gly35Arg)
- GGT1:ENST00000406383.2:c.1135G>A:p.(Gly379Arg)
- Pathogenicity Data:
- Best Score: 0.862
- Polyphen2: 0.005 (B)
- SIFT: 0.138 (T)
- Frequency Data:
- TOPMed: 0.0016%
- gnomAD_E_AFR: 0.0068%
- gnomAD_E_NFE: 0.0036%
- gnomAD_E_SAS: 0.0066%
- Transcripts:
- GGT1:ENST00000248923.4:c.1093C>A:p.(Pro365Thr)
- GGT1:ENST00000400380.1:c.1093C>A:p.(Pro365Thr)
- GGT1:ENST00000400382.1:c.1093C>A:p.(Pro365Thr)
- GGT1:ENST00000400383.1:c.1093C>A:p.(Pro365Thr)
- GGT1:ENST00000401885.1:c.61C>A:p.(Pro21Thr)
- GGT1:ENST00000403838.1:c.61C>A:p.(Pro21Thr)
- GGT1:ENST00000404223.1:c.61C>A:p.(Pro21Thr)
- GGT1:ENST00000404532.1:c.61C>A:p.(Pro21Thr)
- GGT1:ENST00000404920.1:c.61C>A:p.(Pro21Thr)
- GGT1:ENST00000406383.2:c.1093C>A:p.(Pro365Thr)
- Pathogenicity Data:
- Best Score: 0.846
- Polyphen2: 0.062 (B)
- SIFT: 0.154 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- GGT1:ENST00000248923.4:c.1563+8G>A:p.?
- GGT1:ENST00000400380.1:c.1563+8G>A:p.?
- GGT1:ENST00000400382.1:c.1563+8G>A:p.?
- GGT1:ENST00000400383.1:c.1563+8G>A:p.?
- GGT1:ENST00000401885.1:c.531+8G>A:p.?
- GGT1:ENST00000403838.1:c.531+8G>A:p.?
- GGT1:ENST00000404223.1:c.612+8G>A:p.?
- GGT1:ENST00000404532.1:c.531+8G>A:p.?
- GGT1:ENST00000404920.1:c.510+8G>A:p.?
- GGT1:ENST00000406383.2:c.1563+8G>A:p.?
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0026%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_NFE: 0.0018%
- gnomAD_G_NFE: 0.0067%
- Transcripts:
- GGT1:ENST00000248923.4:c.1337-8G>A:p.?
- GGT1:ENST00000400380.1:c.1337-8G>A:p.?
- GGT1:ENST00000400382.1:c.1337-8G>A:p.?
- GGT1:ENST00000400383.1:c.1337-8G>A:p.?
- GGT1:ENST00000401885.1:c.305-8G>A:p.?
- GGT1:ENST00000403838.1:c.305-8G>A:p.?
- GGT1:ENST00000404223.1:c.305-8G>A:p.?
- GGT1:ENST00000404532.1:c.305-8G>A:p.?
- GGT1:ENST00000404920.1:c.305-8G>A:p.?
- GGT1:ENST00000406383.2:c.1337-8G>A:p.?
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0026%
- ESP EA: 0.0234%
- ESP All: 0.0155%
- ExAC NFE: 0.0032%
- gnomAD_E_NFE: 0.0018%
- Transcripts:
- GGT1:ENST00000248923.4:c.1159G>A:p.(Val387Ile)
- GGT1:ENST00000400380.1:c.1159G>A:p.(Val387Ile)
- GGT1:ENST00000400382.1:c.1159G>A:p.(Val387Ile)
- GGT1:ENST00000400383.1:c.1159G>A:p.(Val387Ile)
- GGT1:ENST00000401885.1:c.127G>A:p.(Val43Ile)
- GGT1:ENST00000403838.1:c.127G>A:p.(Val43Ile)
- GGT1:ENST00000404223.1:c.127G>A:p.(Val43Ile)
- GGT1:ENST00000404532.1:c.127G>A:p.(Val43Ile)
- GGT1:ENST00000404920.1:c.127G>A:p.(Val43Ile)
- GGT1:ENST00000406383.2:c.1159G>A:p.(Val387Ile)
- Pathogenicity Data:
- Best Score: 0.786
- Polyphen2: 0.006 (B)
- Mutation Taster: 0.678
- SIFT: 0.214 (T)
- Frequency Data:
- gnomAD_E_AFR: 0.0075%
- gnomAD_E_AMR: 0.0093%
- gnomAD_E_NFE: 0.0058%
- Transcripts:
- GGT1:ENST00000248923.4:c.1081G>A:p.(Asp361Asn)
- GGT1:ENST00000400380.1:c.1081G>A:p.(Asp361Asn)
- GGT1:ENST00000400382.1:c.1081G>A:p.(Asp361Asn)
- GGT1:ENST00000400383.1:c.1081G>A:p.(Asp361Asn)
- GGT1:ENST00000401885.1:c.49G>A:p.(Asp17Asn)
- GGT1:ENST00000403838.1:c.49G>A:p.(Asp17Asn)
- GGT1:ENST00000404223.1:c.49G>A:p.(Asp17Asn)
- GGT1:ENST00000404532.1:c.49G>A:p.(Asp17Asn)
- GGT1:ENST00000404920.1:c.49G>A:p.(Asp17Asn)
- GGT1:ENST00000406383.2:c.1081G>A:p.(Asp361Asn)
- Pathogenicity Data:
- Best Score: 0.694
- Polyphen2: 0.002 (B)
- SIFT: 0.306 (T)
- Frequency Data:
- gnomAD_E_NFE: 0.0018%
- gnomAD_E_SAS: 0.0033%
- gnomAD_G_AFR: 0.0117%
- gnomAD_G_NFE: 0.0141%
- Transcripts:
- GGT1:ENST00000248923.4:c.1114G>A:p.(Glu372Lys)
- GGT1:ENST00000400380.1:c.1114G>A:p.(Glu372Lys)
- GGT1:ENST00000400382.1:c.1114G>A:p.(Glu372Lys)
- GGT1:ENST00000400383.1:c.1114G>A:p.(Glu372Lys)
- GGT1:ENST00000401885.1:c.82G>A:p.(Glu28Lys)
- GGT1:ENST00000403838.1:c.82G>A:p.(Glu28Lys)
- GGT1:ENST00000404223.1:c.82G>A:p.(Glu28Lys)
- GGT1:ENST00000404532.1:c.82G>A:p.(Glu28Lys)
- GGT1:ENST00000404920.1:c.82G>A:p.(Glu28Lys)
- GGT1:ENST00000406383.2:c.1114G>A:p.(Glu372Lys)
- Pathogenicity Data:
- Best Score: 0.798
- Polyphen2: 0.069 (B)
- SIFT: 0.202 (T)
- Frequency Data:
- 1000Genomes: 0.5990%
- TOPMed: 0.8210%
- ESP AA: 0.2729%
- ESP EA: 1.4109%
- ESP All: 1.0251%
- gnomAD_E_AFR: 0.2311%
- gnomAD_E_AMR: 0.4946%
- gnomAD_E_EAS: 0.0464%
- gnomAD_E_FIN: 0.5790%
- gnomAD_E_NFE: 1.2071%
- gnomAD_E_OTH: 0.8775%
- gnomAD_E_SAS: 1.4254%
- gnomAD_G_AFR: 0.3216%
- gnomAD_G_AMR: 0.9592%
- gnomAD_G_FIN: 0.6300%
- gnomAD_G_NFE: 1.3012%
- gnomAD_G_OTH: 0.8180%
- Transcripts:
- GGT1:ENST00000248923.4:c.1425A>G:p.(=)
- GGT1:ENST00000400380.1:c.1425A>G:p.(=)
- GGT1:ENST00000400382.1:c.1425A>G:p.(=)
- GGT1:ENST00000400383.1:c.1425A>G:p.(=)
- GGT1:ENST00000401885.1:c.393A>G:p.(=)
- GGT1:ENST00000403838.1:c.393A>G:p.(=)
- GGT1:ENST00000404223.1:c.393A>G:p.(=)
- GGT1:ENST00000404532.1:c.393A>G:p.(=)
- GGT1:ENST00000406383.2:c.1425A>G:p.(=)
- GGT1:ENST00000404920.1:c.360+33A>G:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0072%
- gnomAD_E_NFE: 0.0063%
- gnomAD_G_AFR: 0.0115%
- gnomAD_G_NFE: 0.0134%
- gnomAD_G_OTH: 0.1020%
- Transcripts:
- GGT1:ENST00000248923.4:c.1293C>T:p.(=)
- GGT1:ENST00000400380.1:c.1293C>T:p.(=)
- GGT1:ENST00000400382.1:c.1293C>T:p.(=)
- GGT1:ENST00000400383.1:c.1293C>T:p.(=)
- GGT1:ENST00000401885.1:c.261C>T:p.(=)
- GGT1:ENST00000403838.1:c.261C>T:p.(=)
- GGT1:ENST00000404223.1:c.261C>T:p.(=)
- GGT1:ENST00000404532.1:c.261C>T:p.(=)
- GGT1:ENST00000404920.1:c.261C>T:p.(=)
- GGT1:ENST00000406383.2:c.1293C>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0200%
- ESP AA: 0.0227%
- ESP EA: 0.1395%
- ESP All: 0.1000%
- ExAC AFR: 0.0485%
- ExAC AMR: 0.1037%
- ExAC FIN: 0.1058%
- ExAC NFE: 0.3389%
- ExAC SAS: 0.1211%
- gnomAD_E_AMR: 0.0209%
- gnomAD_E_FIN: 0.0494%
- gnomAD_E_NFE: 0.0741%
- gnomAD_E_SAS: 0.0163%
- gnomAD_G_NFE: 0.0402%
- gnomAD_G_OTH: 0.1022%
- Transcripts:
- GGT1:ENST00000248923.4:c.1365G>A:p.(=)
- GGT1:ENST00000400380.1:c.1365G>A:p.(=)
- GGT1:ENST00000400382.1:c.1365G>A:p.(=)
- GGT1:ENST00000400383.1:c.1365G>A:p.(=)
- GGT1:ENST00000401885.1:c.333G>A:p.(=)
- GGT1:ENST00000403838.1:c.333G>A:p.(=)
- GGT1:ENST00000404223.1:c.333G>A:p.(=)
- GGT1:ENST00000404532.1:c.333G>A:p.(=)
- GGT1:ENST00000404920.1:c.333G>A:p.(=)
- GGT1:ENST00000406383.2:c.1365G>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0399%
- TOPMed: 0.0299%
- ESP AA: 0.0227%
- ESP All: 0.0077%
- ExAC AFR: 0.0106%
- ExAC AMR: 0.0087%
- ExAC EAS: 0.7548%
- gnomAD_E_AFR: 0.0066%
- gnomAD_E_AMR: 0.0119%
- gnomAD_E_EAS: 0.6785%
- gnomAD_E_NFE: 0.0009%
- gnomAD_G_AFR: 0.0115%
- gnomAD_G_EAS: 0.6180%
- Proximity score 0.503 in interactome to ARL3 and phenotypic similarity 0.613 to Joubert syndrome associated with ARL3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001829, Foot polydactyly
- HP:0001363, Craniosynostosis - HP:0004422, Biparietal narrowing
- HP:0011304, Broad thumb - HP:0001161, Hand polydactyly
- HP:0010055, Broad hallux - HP:0001829, Foot polydactyly
- Proximity score 0.503 in interactome to ARL3 and phenotypic similarity 0.265 to mouse mutant of ARL3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0008518, retinal outer nuclear layer degeneration
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.754
Phenotype Score: 0.503
Variant Score: 1.000
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.509
Phenotype Score: 0.503
Variant Score: 0.882
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0066%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_EAS: 0.0118%
- gnomAD_E_FIN: 0.0322%
- gnomAD_E_NFE: 0.0367%
- gnomAD_E_OTH: 0.0186%
- gnomAD_E_SAS: 0.0066%
- gnomAD_G_EAS: 0.2528%
- gnomAD_G_FIN: 0.2900%
- gnomAD_G_NFE: 0.0472%
- gnomAD_G_OTH: 0.2070%
- Phenotypic similarity 0.274 to Neuronopathy, distal hereditary motor, type IX associated with WARS1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux - HP:0001761, Pes cavus
- Phenotypic similarity 0.299 to mouse mutant involving WARS1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001303, abnormal lens morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.506 in interactome to TARS1 and phenotypic similarity 0.712 to Trichothiodystrophy associated with TARS1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001217, Clubbing
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0001217, Clubbing
- HP:0010055, Broad hallux - HP:0001217, Clubbing
- Known diseases:
- OMIM:617721 Neuronopathy, distal hereditary motor, type IX - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.753
Phenotype Score: 0.506
Variant Score: 0.996
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.274 to OMIM:617721 Neuronopathy, distal hereditary motor, type IX
- Transcripts:
- WARS1:ENST00000344102.5:c.1220G>A:p.(Arg407Gln)
- WARS1:ENST00000355338.2:c.1343G>A:p.(Arg448Gln)
- WARS1:ENST00000358655.4:c.1220G>A:p.(Arg407Gln)
- WARS1:ENST00000392882.2:c.1343G>A:p.(Arg448Gln)
- WARS1:ENST00000556645.1:c.1220G>A:p.(Arg407Gln)
- WARS1:ENST00000557135.1:c.1343G>A:p.(Arg448Gln)
- Pathogenicity Data:
- Best Score: 0.999993
- Polyphen2: 0.048 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.015 (D)
- Frequency Data:
- TOPMed: 0.0019%
- UK10K: 0.0132%
- ExAC FIN: 0.0302%
- ExAC NFE: 0.0030%
- gnomAD_E_EAS: 0.0058%
- gnomAD_E_FIN: 0.0224%
- gnomAD_E_NFE: 0.0037%
- gnomAD_E_OTH: 0.0183%
- Proximity score 0.502 in interactome to PRKCZ and phenotypic similarity 0.667 to 1p36 deletion syndrome associated with PRKCZ.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0000270, Delayed cranial suture closure
- HP:0011304, Broad thumb - HP:0100490, Camptodactyly of finger
- HP:0010055, Broad hallux - HP:0001829, Foot polydactyly
- Proximity score 0.502 in interactome to PRKCZ and phenotypic similarity 0.276 to mouse mutant of PRKCZ.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001289, persistence of hyaloid vascular system
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.752
Phenotype Score: 0.502
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.827 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.003 (D)
- Frequency Data:
- No frequency data
- Proximity score 0.516 in interactome to SPRY4 and phenotypic similarity 0.295 to Kallmann syndrome associated with SPRY4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux - HP:0001761, Pes cavus
- Proximity score 0.516 in interactome to SPRY4 and phenotypic similarity 0.911 to mouse mutant of SPRY4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002544, brachydactyly
- HP:0001363, Craniosynostosis - MP:0001312, abnormal cornea morphology
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.751
Phenotype Score: 0.516
Variant Score: 0.983
- Transcripts:
- PTPRB:ENST00000261266.5:c.2483G>A:p.(Arg828His)
- PTPRB:ENST00000334414.6:c.3137G>A:p.(Arg1046His)
- PTPRB:ENST00000451516.2:c.2213G>A:p.(Arg738His)
- PTPRB:ENST00000538708.1:c.2483G>A:p.(Arg828His)
- PTPRB:ENST00000550358.1:c.2873G>A:p.(Arg958His)
- PTPRB:ENST00000550857.1:c.2213G>A:p.(Arg738His)
- PTPRB:ENST00000551525.1:c.3134G>A:p.(Arg1045His)
- Pathogenicity Data:
- Best Score: 0.992
- Polyphen2: 0.707 (P)
- SIFT: 0.008 (D)
- Frequency Data:
- TOPMed: 0.0034%
- ExAC AFR: 0.0104%
- ExAC EAS: 0.0235%
- ExAC NFE: 0.0015%
- gnomAD_E_AFR: 0.0131%
- gnomAD_E_EAS: 0.0174%
- gnomAD_E_NFE: 0.0036%
- gnomAD_E_OTH: 0.0366%
- gnomAD_G_AFR: 0.0115%
- gnomAD_G_EAS: 0.0617%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.611
Phenotype Score: 0.516
Variant Score: 0.912
- Transcripts:
- PTPRB:ENST00000261266.5:c.2483G>A:p.(Arg828His)
- PTPRB:ENST00000334414.6:c.3137G>A:p.(Arg1046His)
- PTPRB:ENST00000451516.2:c.2213G>A:p.(Arg738His)
- PTPRB:ENST00000538708.1:c.2483G>A:p.(Arg828His)
- PTPRB:ENST00000550358.1:c.2873G>A:p.(Arg958His)
- PTPRB:ENST00000550857.1:c.2213G>A:p.(Arg738His)
- PTPRB:ENST00000551525.1:c.3134G>A:p.(Arg1045His)
- Pathogenicity Data:
- Best Score: 0.992
- Polyphen2: 0.707 (P)
- SIFT: 0.008 (D)
- Frequency Data:
- TOPMed: 0.0034%
- ExAC AFR: 0.0104%
- ExAC EAS: 0.0235%
- ExAC NFE: 0.0015%
- gnomAD_E_AFR: 0.0131%
- gnomAD_E_EAS: 0.0174%
- gnomAD_E_NFE: 0.0036%
- gnomAD_E_OTH: 0.0366%
- gnomAD_G_AFR: 0.0115%
- gnomAD_G_EAS: 0.0617%
- Transcripts:
- PTPRB:ENST00000261266.5:c.5174C>T:p.(Pro1725Leu)
- PTPRB:ENST00000334414.6:c.5828C>T:p.(Pro1943Leu)
- PTPRB:ENST00000451516.2:c.4904C>T:p.(Pro1635Leu)
- PTPRB:ENST00000538708.1:c.4904C>T:p.(Pro1635Leu)
- PTPRB:ENST00000550358.1:c.5564C>T:p.(Pro1855Leu)
- PTPRB:ENST00000550857.1:c.4904C>T:p.(Pro1635Leu)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.260 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.070 (T)
- Frequency Data:
- 1000Genomes: 0.0998%
- TOPMed: 0.0249%
- ExAC EAS: 0.7773%
- ExAC NFE: 0.0048%
- gnomAD_E_AFR: 0.0066%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_EAS: 0.6796%
- gnomAD_E_NFE: 0.0018%
- gnomAD_G_AFR: 0.0115%
- gnomAD_G_EAS: 0.6173%
- gnomAD_G_OTH: 0.1018%
- Proximity score 0.501 in interactome to PIBF1 and phenotypic similarity 0.613 to Joubert syndrome associated with PIBF1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001829, Foot polydactyly
- HP:0001363, Craniosynostosis - HP:0004422, Biparietal narrowing
- HP:0011304, Broad thumb - HP:0001161, Hand polydactyly
- HP:0010055, Broad hallux - HP:0001829, Foot polydactyly
- Proximity score 0.501 in interactome to PIBF1 and phenotypic similarity 0.278 to mouse mutant of PIBF1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001303, abnormal lens morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.751
Phenotype Score: 0.501
Variant Score: 1.000
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.638
Phenotype Score: 0.501
Variant Score: 0.941
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.947
- SIFT: 0.053 (D)
- Frequency Data:
- gnomAD_G_AFR: 0.2033%
- gnomAD_G_AMR: 0.1462%
- gnomAD_G_EAS: 0.4058%
- gnomAD_G_FIN: 0.0353%
- gnomAD_G_NFE: 0.0369%
- Transcripts:
- MUC16:ENST00000397910.4:c.38214G>A:p.(Met12738Ile)
- Pathogenicity Data:
- Best Score: 0.849
- SIFT: 0.151 (T)
- Frequency Data:
- gnomAD_G_AFR: 0.5814%
- gnomAD_G_AMR: 0.3268%
- gnomAD_G_EAS: 0.1471%
- gnomAD_G_FIN: 0.8368%
- gnomAD_G_NFE: 0.2994%
- gnomAD_G_OTH: 0.2370%
- Pathogenicity Data:
- Best Score: 0.30900002
- SIFT: 0.691 (T)
- Frequency Data:
- gnomAD_G_AFR: 0.3492%
- gnomAD_G_AMR: 0.3106%
- gnomAD_G_EAS: 0.4401%
- gnomAD_G_FIN: 0.1130%
- gnomAD_G_NFE: 0.0908%
- gnomAD_G_OTH: 0.1214%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_G_AFR: 0.2472%
- gnomAD_G_AMR: 0.1458%
- gnomAD_G_EAS: 0.4052%
- gnomAD_G_FIN: 0.0355%
- gnomAD_G_NFE: 0.0516%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_G_AFR: 0.3268%
- gnomAD_G_AMR: 0.3021%
- gnomAD_G_EAS: 0.4244%
- gnomAD_G_FIN: 0.0738%
- gnomAD_G_NFE: 0.0748%
- gnomAD_G_OTH: 0.1214%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_G_AFR: 0.5561%
- gnomAD_G_AMR: 0.3268%
- gnomAD_G_EAS: 0.3559%
- gnomAD_G_FIN: 0.2268%
- gnomAD_G_NFE: 0.0764%
- gnomAD_G_OTH: 0.1256%
- Proximity score 0.501 in interactome to ATF4 and phenotypic similarity 0.648 to mouse mutant of ATF4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0005298, abnormal clavicle morphology
- HP:0001363, Craniosynostosis - MP:0030388, large fontanelles
- HP:0011304, Broad thumb - MP:0005298, abnormal clavicle morphology
- HP:0010055, Broad hallux - MP:0005298, abnormal clavicle morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.751
Phenotype Score: 0.501
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 0.999989
- Polyphen2: 0.536 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.003 (D)
- Frequency Data:
- TOPMed: 0.0019%
- gnomAD_E_SAS: 0.0032%
- Proximity score 0.501 in interactome to PRKCZ and phenotypic similarity 0.667 to 1p36 deletion syndrome associated with PRKCZ.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0000270, Delayed cranial suture closure
- HP:0011304, Broad thumb - HP:0100490, Camptodactyly of finger
- HP:0010055, Broad hallux - HP:0001829, Foot polydactyly
- Proximity score 0.501 in interactome to PRKCZ and phenotypic similarity 0.276 to mouse mutant of PRKCZ.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001289, persistence of hyaloid vascular system
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.750
Phenotype Score: 0.501
Variant Score: 0.999
- Pathogenicity Data:
- Best Score: 0.99909
- Polyphen2: 0.212 (B)
- Mutation Taster: 0.999 (P)
- SIFT: 0.082 (T)
- Frequency Data:
- No frequency data
- Proximity score 0.501 in interactome to TRIO and phenotypic similarity 0.681 to Intellectual developmental disorder, autosomal dominant 44, with microcephaly associated with TRIO.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001182, Tapered finger
- HP:0010055, Broad hallux - HP:0004691, 2-3 toe syndactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.750
Phenotype Score: 0.501
Variant Score: 1.000
- Transcripts:
- CARMIL1:ENST00000329474.6:c.1214C>G:p.(Ser405Cys)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.944 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.001 (D)
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.280 to mouse mutant involving PAK1IP1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0000455, abnormal maxilla morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.501 in interactome to PLCB3 and phenotypic similarity 0.614 to Spondylometaphyseal dysplasia with corneal dystrophy associated with PLCB3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001156, Brachydactyly
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Proximity score 0.501 in interactome to PLCB3 and phenotypic similarity 0.332 to fish mutant of PLCB3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - ZP:0005101, palatoquadrate cartilage curved lateral, abnormal
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.750
Phenotype Score: 0.501
Variant Score: 1.000
- Transcripts:
- PAK1IP1:ENST00000379568.3:c.661G>T:p.(Ala221Ser)
- Pathogenicity Data:
- Best Score: 0.999998
- Polyphen2: 0.464 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.020 (D)
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.387 to mouse mutant involving ST18.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0003345, decreased rib number
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0003345, decreased rib number
- HP:0010055, Broad hallux - MP:0003345, decreased rib number
- Proximity score 0.500 in interactome to SOX14 and phenotypic similarity 0.755 to mouse mutant of SOX14.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.750
Phenotype Score: 0.500
Variant Score: 1.000
- Transcripts:
- ST18:ENST00000276480.7:c.3008C>T:p.(Pro1003Leu)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.998 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- Proximity score 0.501 in interactome to SCARF2 and phenotypic similarity 0.704 to Van den Ende-Gupta syndrome associated with SCARF2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001166, Arachnodactyly
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0006236, Slender metacarpals
- HP:0010055, Broad hallux - HP:0001847, Long hallux
- Proximity score 0.501 in interactome to SCARF2 and phenotypic similarity 0.487 to mouse mutant of SCARF2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0004357, long tibia
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0004357, long tibia
- HP:0010055, Broad hallux - MP:0004357, long tibia
- Known diseases:
- OMIM:617027 Hyperaldosteronism, familial, type IV - autosomal dominant
- ORPHA:64280 Childhood absence epilepsy - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.750
Phenotype Score: 0.501
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 0.999947
- Polyphen2: 0.991 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.001 (D)
- Frequency Data:
- TOPMed: 0.0008%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.003
Phenotype Score: 0.250
Variant Score: 0.514
- Pathogenicity Data:
- Best Score: 0.999947
- Polyphen2: 0.991 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.001 (D)
- Frequency Data:
- TOPMed: 0.0008%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.4593%
- TOPMed: 0.0816%
- ExAC AMR: 0.0093%
- ExAC EAS: 1.8416%
- ExAC OTH: 0.1458%
- ExAC SAS: 0.0072%
- gnomAD_E_AMR: 0.0063%
- gnomAD_E_EAS: 1.7876%
- gnomAD_E_OTH: 0.0205%
- gnomAD_E_SAS: 0.0104%
- gnomAD_G_EAS: 1.8496%
- Proximity score 0.500 in interactome to NEK1 and phenotypic similarity 0.813 to Orofaciodigital syndrome type 2 associated with NEK1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0006101, Finger syndactyly
- HP:0001363, Craniosynostosis - HP:0410033, Unilateral alveolar cleft of maxilla
- HP:0011304, Broad thumb - HP:0010068, Broad first metatarsal
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
- Proximity score 0.500 in interactome to NEK1 and phenotypic similarity 0.541 to mouse mutant of NEK1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0004509, abnormal pelvic girdle bone morphology
- HP:0001363, Craniosynostosis - MP:0000438, abnormal cranium morphology
- HP:0011304, Broad thumb - MP:0004509, abnormal pelvic girdle bone morphology
- HP:0010055, Broad hallux - MP:0004509, abnormal pelvic girdle bone morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.749
Phenotype Score: 0.500
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.333 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.038 (D)
- Frequency Data:
- No frequency data
- Proximity score 0.500 in interactome to NHS and phenotypic similarity 0.623 to Nance-Horan syndrome associated with NHS.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001500, Broad finger
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001500, Broad finger
- HP:0010055, Broad hallux - HP:0001500, Broad finger
- Proximity score 0.500 in interactome to NHS and phenotypic similarity 0.346 to mouse mutant of NHS.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001303, abnormal lens morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.749
Phenotype Score: 0.500
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 0.999999
- Polyphen2: 0.011 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.129 (T)
- Frequency Data:
- No frequency data
- Proximity score 0.501 in interactome to B3GAT3 and phenotypic similarity 0.761 to Multiple joint dislocations, short stature, craniofacial dysmorphism, with or without congenital heart defects associated with B3GAT3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001822, Hallux valgus
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0001222, Spatulate thumbs
- HP:0010055, Broad hallux - HP:0001822, Hallux valgus
- Proximity score 0.501 in interactome to B3GAT3 and phenotypic similarity 0.407 to fish mutant of B3GAT3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - ZP:0001216, head cuboid, abnormal
- HP:0011304, Broad thumb - ZP:0000875, cleithrum malformed, abnormal
- HP:0010055, Broad hallux -
- Known diseases:
- OMIM:138500 Hyperglycinuria - autosomal dominant
- OMIM:242600 Iminoglycinuria, digenic - autosomal recessive
- ORPHA:42062 Iminoglycinuria - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.749
Phenotype Score: 0.501
Variant Score: 0.999
- Pathogenicity Data:
- Best Score: 0.999254
- Polyphen2: 0.974 (D)
- Mutation Taster: 0.999 (P)
- SIFT: 0.001 (D)
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.046
Phenotype Score: 0.501
Variant Score: 0.549
- Pathogenicity Data:
- Best Score: 0.999254
- Polyphen2: 0.974 (D)
- Mutation Taster: 0.999 (P)
- SIFT: 0.001 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0042%
- ESP AA: 0.0227%
- ESP All: 0.0077%
- ExAC AFR: 0.0194%
- ExAC NFE: 0.0015%
- ExAC OTH: 0.1111%
- gnomAD_E_AFR: 0.0065%
- gnomAD_E_EAS: 0.0058%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_OTH: 0.0183%
- gnomAD_G_AFR: 0.0115%
- gnomAD_G_OTH: 0.1018%
- Proximity score 0.500 in interactome to COLGALT1 and phenotypic similarity 0.670 to mouse mutant of COLGALT1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000554, abnormal carpal bone morphology
- HP:0001363, Craniosynostosis - MP:0002092, abnormal eye morphology
- HP:0011304, Broad thumb - MP:0000554, abnormal carpal bone morphology
- HP:0010055, Broad hallux - MP:0000554, abnormal carpal bone morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.749
Phenotype Score: 0.500
Variant Score: 1.000
- Transcripts:
- ERO1A:ENST00000395686.3:c.159T>G:p.(Ile53Met)
- Pathogenicity Data:
- Best Score: 0.999999
- Polyphen2: 0.977 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.002 (D)
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.245 to mouse mutant involving LEPROT.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0010123, increased bone mineral content
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.500 in interactome to RDH10 and phenotypic similarity 0.880 to mouse mutant of RDH10.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002544, brachydactyly
- HP:0001363, Craniosynostosis - MP:0001286, abnormal eye development
- HP:0011304, Broad thumb - MP:0000564, syndactyly
- HP:0010055, Broad hallux - MP:0000564, syndactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.749
Phenotype Score: 0.500
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.982 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.118 (T)
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.247 to mouse mutant involving MAL.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001330, abnormal optic nerve morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.500 in interactome to ALX3 and phenotypic similarity 0.685 to Frontonasal dysplasia 1 associated with ALX3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0009099, Median cleft palate
- HP:0011304, Broad thumb - HP:0001162, Postaxial hand polydactyly
- HP:0010055, Broad hallux - HP:0030084, Clinodactyly
- Proximity score 0.500 in interactome to ALX3 and phenotypic similarity 0.270 to mouse mutant of ALX3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0009264, failure of eyelid fusion
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.749
Phenotype Score: 0.500
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.090 (B)
- Mutation Taster: 0.822
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- Proximity score 0.500 in interactome to RASA2 and phenotypic similarity 0.642 to Noonan syndrome associated with RASA2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0004209, Clinodactyly of the 5th finger
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.749
Phenotype Score: 0.500
Variant Score: 1.000
- Transcripts:
- ARHGEF5:ENST00000056217.5:c.7_28dup:p.(Ala10Glyfs*2)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.500 in interactome to LEMD3 and phenotypic similarity 0.709 to Buschke-Ollendorff syndrome associated with LEMD3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010554, Cutaneous finger syndactyly
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0010554, Cutaneous finger syndactyly
- HP:0010055, Broad hallux - HP:0010554, Cutaneous finger syndactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.749
Phenotype Score: 0.500
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.316 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.233 (T)
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.749
Phenotype Score: 0.500
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.316 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.233 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.792 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.063 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.000 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.585 (T)
- Frequency Data:
- ExAC SAS: 0.0061%
- gnomAD_E_SAS: 0.0032%
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.766 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.001 (D)
- Frequency Data:
- TOPMed: 0.0011%
- ExAC SAS: 0.0061%
- gnomAD_E_AFR: 0.0065%
- gnomAD_E_SAS: 0.0032%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.253 to mouse mutant involving PMEL.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0010192, abnormal retinal melanin granule morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.501 in interactome to CSNK2A1 and phenotypic similarity 0.665 to Okur-Chung neurodevelopmental syndrome associated with CSNK2A1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0030084, Clinodactyly
- HP:0010055, Broad hallux - HP:0030084, Clinodactyly
- Proximity score 0.501 in interactome to CSNK2A1 and phenotypic similarity 0.535 to mouse mutant of CSNK2A1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0005650, abnormal limb bud morphology
- HP:0001363, Craniosynostosis - MP:0011495, abnormal head shape
- HP:0011304, Broad thumb - MP:0005650, abnormal limb bud morphology
- HP:0010055, Broad hallux - MP:0005650, abnormal limb bud morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.749
Phenotype Score: 0.501
Variant Score: 0.999
- Transcripts:
- PMEL:ENST00000360714.4:c.1043C>A:p.(Thr348Asn)
- PMEL:ENST00000449260.2:c.1043C>A:p.(Thr348Asn)
- PMEL:ENST00000536427.1:c.1043C>A:p.(Thr348Asn)
- PMEL:ENST00000539511.1:c.785C>A:p.(Thr262Asn)
- PMEL:ENST00000548493.1:c.1043C>A:p.(Thr348Asn)
- PMEL:ENST00000548747.1:c.1043C>A:p.(Thr348Asn)
- PMEL:ENST00000550464.1:c.785C>A:p.(Thr262Asn)
- PMEL:ENST00000552882.1:c.1043C>A:p.(Thr348Asn)
- PMEL:ENST00000550447.1:c.358+1213C>A:p.(=)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.895 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- TOPMed: 0.0004%
- gnomAD_E_EAS: 0.0058%
- Proximity score 0.500 in interactome to RNF113A and phenotypic similarity 0.712 to Trichothiodystrophy associated with RNF113A.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001217, Clubbing
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0001217, Clubbing
- HP:0010055, Broad hallux - HP:0001217, Clubbing
- Proximity score 0.500 in interactome to RNF113A and phenotypic similarity 0.262 to mouse mutant of RNF113A.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0002792, abnormal retinal vasculature morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.749
Phenotype Score: 0.500
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 0.999993
- Polyphen2: 0.770 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.014 (D)
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.356
Phenotype Score: 0.500
Variant Score: 0.817
- Pathogenicity Data:
- Best Score: 0.999993
- Polyphen2: 0.770 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.014 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.899
- Polyphen2: 0.013 (B)
- SIFT: 0.101 (T)
- Frequency Data:
- 1000Genomes: 1.1580%
- TOPMed: 1.1580%
- gnomAD_E_AFR: 0.0133%
- gnomAD_E_EAS: 0.0180%
- gnomAD_E_FIN: 0.0943%
- gnomAD_E_NFE: 0.0036%
- gnomAD_E_SAS: 0.0066%
- Proximity score 0.500 in interactome to PRKAR1A and phenotypic similarity 0.684 to Acrodysostosis 1, with or without hormone resistance associated with PRKAR1A.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0004490, Calvarial hyperostosis
- HP:0011304, Broad thumb - HP:0009803, Short phalanx of finger
- HP:0010055, Broad hallux - HP:0001847, Long hallux
- Proximity score 0.500 in interactome to PRKAR1A and phenotypic similarity 0.852 to mouse mutant of PRKAR1A.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002544, brachydactyly
- HP:0001363, Craniosynostosis - MP:0003419, delayed endochondral bone ossification
- HP:0011304, Broad thumb - MP:0002544, brachydactyly
- HP:0010055, Broad hallux - MP:0002544, brachydactyly
- Known diseases:
- OMIM:149700 ?Lacrimal duct defect (unconfirmed)
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.749
Phenotype Score: 0.500
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.997 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.006 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.999978
- Polyphen2: 0.485 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.137 (T)
- Frequency Data:
- gnomAD_E_NFE: 0.0009%
AUTOSOMAL_DOMINANT
Exomiser Score: 0.182
Phenotype Score: 0.250
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.997 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.006 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- Frequency Data:
- ExAC NFE: 0.0015%
- gnomAD_E_NFE: 0.0009%
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 1.000 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.007 (D)
- Frequency Data:
- TOPMed: 0.0004%
- gnomAD_E_NFE: 0.0018%
- Pathogenicity Data:
- Best Score: 0.999686
- Polyphen2: 0.060 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.831 (T)
- Frequency Data:
- TOPMed: 0.0008%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_SAS: 0.0033%
- Pathogenicity Data:
- Best Score: 0.999878
- Polyphen2: 0.999 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.230 (T)
- Frequency Data:
- gnomAD_E_AFR: 0.0066%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_NFE: 0.0036%
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- Frequency Data:
- TOPMed: 0.0016%
- gnomAD_E_NFE: 0.0009%
- gnomAD_G_AFR: 0.0114%
- gnomAD_G_NFE: 0.0067%
- Pathogenicity Data:
- Best Score: 0.997634
- Polyphen2: 0.293 (B)
- Mutation Taster: 0.998 (P)
- SIFT: 0.051 (D)
- Frequency Data:
- TOPMed: 0.0045%
- gnomAD_E_NFE: 0.0045%
- gnomAD_E_SAS: 0.0032%
- Pathogenicity Data:
- Best Score: 0.995157
- Polyphen2: 0.014 (B)
- Mutation Taster: 0.995 (P)
- SIFT: 0.307 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.99601
- Polyphen2: 0.790 (P)
- Mutation Taster: 0.996 (P)
- SIFT: 0.050 (D)
- Frequency Data:
- TOPMed: 0.0015%
- gnomAD_E_SAS: 0.0065%
- Pathogenicity Data:
- Best Score: 0.995
- Polyphen2: 0.035 (B)
- SIFT: 0.005 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.984
- Polyphen2: 0.024 (B)
- SIFT: 0.016 (D)
- Frequency Data:
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_SAS: 0.0032%
- Pathogenicity Data:
- Best Score: 0.973426
- Polyphen2: 0.403 (B)
- Mutation Taster: 0.973 (P)
- SIFT: 0.124 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.999675
- Polyphen2: 0.164 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.002 (D)
- Frequency Data:
- 1000Genomes: 0.1997%
- TOPMed: 0.1997%
- ExAC AFR: 0.0971%
- ExAC AMR: 0.0699%
- ExAC EAS: 0.0701%
- ExAC FIN: 0.0156%
- ExAC NFE: 0.0347%
- ExAC OTH: 0.3348%
- ExAC SAS: 0.0489%
- gnomAD_E_AFR: 0.0393%
- gnomAD_E_AMR: 0.1074%
- gnomAD_E_EAS: 0.0466%
- gnomAD_E_NFE: 0.0243%
- gnomAD_E_OTH: 0.0913%
- gnomAD_E_SAS: 0.0261%
- gnomAD_G_AFR: 0.1048%
- gnomAD_G_AMR: 0.1205%
- gnomAD_G_EAS: 0.0623%
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 1.000 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.003 (D)
- Frequency Data:
- gnomAD_E_AFR: 0.1326%
- gnomAD_E_AMR: 0.1387%
- gnomAD_E_EAS: 0.1428%
- gnomAD_E_FIN: 0.5665%
- gnomAD_E_NFE: 0.3553%
- gnomAD_E_OTH: 0.1934%
- gnomAD_E_SAS: 0.1694%
- gnomAD_G_AFR: 0.0235%
- gnomAD_G_AMR: 0.2488%
- gnomAD_G_FIN: 0.3088%
- gnomAD_G_NFE: 0.1333%
- Pathogenicity Data:
- Best Score: 0.78499997
- Polyphen2: 0.001 (B)
- SIFT: 0.215 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.728636
- Polyphen2: 0.004 (B)
- Mutation Taster: 0.729
- Frequency Data:
- TOPMed: 0.0023%
- gnomAD_E_AFR: 0.0065%
- gnomAD_E_NFE: 0.0018%
- Pathogenicity Data:
- Best Score: 0.905
- Polyphen2: 0.476 (P)
- Mutation Taster: 0.840
- SIFT: 0.095 (T)
- Frequency Data:
- gnomAD_E_AFR: 0.3207%
- gnomAD_E_AMR: 0.1427%
- gnomAD_E_EAS: 0.4202%
- gnomAD_E_FIN: 1.0340%
- gnomAD_E_NFE: 0.3358%
- gnomAD_E_OTH: 0.1567%
- gnomAD_E_SAS: 0.0703%
- gnomAD_G_AFR: 0.1404%
- gnomAD_G_AMR: 0.3713%
- gnomAD_G_EAS: 0.1918%
- gnomAD_G_FIN: 0.2158%
- gnomAD_G_NFE: 0.2035%
- Pathogenicity Data:
- Best Score: 0.15100002
- Polyphen2: 0.006 (B)
- SIFT: 0.849 (T)
- Frequency Data:
- TOPMed: 0.0068%
- ESP EA: 0.0116%
- ESP All: 0.0077%
- gnomAD_E_EAS: 0.0058%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_SAS: 0.0162%
- gnomAD_G_AFR: 0.0115%
- gnomAD_G_NFE: 0.0067%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0004%
- gnomAD_E_NFE: 0.0009%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0019%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_SAS: 0.0037%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
- ExAC AMR: 0.0089%
- gnomAD_E_AFR: 0.0069%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_EAS: 0.0058%
- gnomAD_E_NFE: 0.0009%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0034%
- ExAC AFR: 0.0105%
- ExAC AMR: 0.0087%
- ExAC NFE: 0.0015%
- gnomAD_E_AFR: 0.0068%
- gnomAD_E_AMR: 0.0060%
- gnomAD_E_NFE: 0.0018%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0196%
- UK10K: 0.0132%
- gnomAD_E_NFE: 0.0269%
- gnomAD_G_AFR: 0.0458%
- gnomAD_G_NFE: 0.0533%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0799%
- TOPMed: 0.0159%
- ESP AA: 0.1135%
- ESP All: 0.0384%
- ExAC AFR: 0.1785%
- ExAC AMR: 0.0087%
- ExAC EAS: 0.0232%
- ExAC NFE: 0.0121%
- ExAC SAS: 0.0304%
- gnomAD_E_AFR: 0.0655%
- gnomAD_E_AMR: 0.0089%
- gnomAD_E_EAS: 0.0116%
- gnomAD_E_NFE: 0.0072%
- gnomAD_E_SAS: 0.0097%
- gnomAD_G_AFR: 0.0344%
- Proximity score 0.500 in interactome to MMP2 and phenotypic similarity 0.638 to Multicentric osteolysis-nodulosis-arthropathy spectrum associated with MMP2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001230, Broad metacarpals
- HP:0001363, Craniosynostosis - HP:0005441, Sclerotic cranial sutures
- HP:0011304, Broad thumb - HP:0001230, Broad metacarpals
- HP:0010055, Broad hallux - HP:0006234, Osteolysis involving tarsal bones
- Proximity score 0.500 in interactome to MMP2 and phenotypic similarity 0.707 to mouse mutant of MMP2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0004686, decreased length of long bones
- HP:0001363, Craniosynostosis - MP:0003840, abnormal coronal suture morphology
- HP:0011304, Broad thumb - MP:0004686, decreased length of long bones
- HP:0010055, Broad hallux - MP:0004686, decreased length of long bones
AUTOSOMAL_DOMINANT
Exomiser Score: 0.749
Phenotype Score: 0.500
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.855 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.004 (D)
- Frequency Data:
- ExAC NFE: 0.0015%
- gnomAD_E_NFE: 0.0009%
- Proximity score 0.500 in interactome to USP7 and phenotypic similarity 0.721 to Hao-Fountain syndrome associated with USP7.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001822, Hallux valgus
- HP:0001363, Craniosynostosis - HP:0000270, Delayed cranial suture closure
- HP:0011304, Broad thumb - HP:0004209, Clinodactyly of the 5th finger
- HP:0010055, Broad hallux - HP:0001822, Hallux valgus
X_RECESSIVE
Exomiser Score: 0.748
Phenotype Score: 0.500
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.034 (B)
- SIFT: 0.000 (D)
- Frequency Data:
- TOPMed: 0.0008%
- ExAC NFE: 0.0024%
- gnomAD_E_NFE: 0.0025%
X_DOMINANT
Exomiser Score: 0.748
Phenotype Score: 0.500
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.034 (B)
- SIFT: 0.000 (D)
- Frequency Data:
- TOPMed: 0.0008%
- ExAC NFE: 0.0024%
- gnomAD_E_NFE: 0.0025%
- Proximity score 0.500 in interactome to PALS1 and phenotypic similarity 0.869 to Non-specific syndromic intellectual disability associated with PALS1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010109, Short hallux
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0011304, Broad thumb
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
- Proximity score 0.500 in interactome to PALS1 and phenotypic similarity 0.331 to fish mutant of PALS1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - ZP:0001253, head surface feature shape, abnormal
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.748
Phenotype Score: 0.500
Variant Score: 1.000
- Transcripts:
- TCERG1L:ENST00000368642.4:c.1357C>T:p.(Arg453Cys)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.998 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.026 (D)
- Frequency Data:
- TOPMed: 0.0034%
- Phenotypic similarity 0.331 to mouse mutant involving ADAL.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.500 in interactome to ADA2 and phenotypic similarity 0.670 to Blackfan-Diamond anemia associated with ADA2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0009778, Short thumb
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001199, Triphalangeal thumb
- HP:0010055, Broad hallux - HP:0001199, Triphalangeal thumb
AUTOSOMAL_DOMINANT
Exomiser Score: 0.747
Phenotype Score: 0.500
Variant Score: 0.999
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.998 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- TOPMed: 0.0008%
- ExAC AFR: 0.0097%
- gnomAD_E_AFR: 0.0065%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_SAS: 0.0032%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.747
Phenotype Score: 0.500
Variant Score: 0.999
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.998 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- TOPMed: 0.0008%
- ExAC AFR: 0.0097%
- gnomAD_E_AFR: 0.0065%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_SAS: 0.0032%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0004%
- gnomAD_E_EAS: 0.0098%
- Phenotypic similarity 0.359 to Monilethrix associated with KRT83.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001597, Abnormality of the nail
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001597, Abnormality of the nail
- HP:0010055, Broad hallux - HP:0001597, Abnormality of the nail
- Proximity score 0.500 in interactome to TGFBR1 and phenotypic similarity 0.749 to Loeys-Dietz syndrome 1 associated with TGFBR1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001166, Arachnodactyly
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0001162, Postaxial hand polydactyly
- HP:0010055, Broad hallux - HP:0001166, Arachnodactyly
- Proximity score 0.500 in interactome to TGFBR1 and phenotypic similarity 0.952 to mouse mutant of TGFBR1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0000081, premature cranial suture closure
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Known diseases:
- OMIM:158000 Monilethrix - autosomal dominant
- OMIM:617756 Erythrokeratodermia variabilis et progressiva 5 - autosomal recessive
- ORPHA:316 Progressive symmetric erythrokeratodermia - autosomal recessive
- ORPHA:573 Monilethrix - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.747
Phenotype Score: 0.500
Variant Score: 0.999
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.359 to ORPHA:573 Monilethrix
- Phenotypic similarity 0.349 to OMIM:158000 Monilethrix
- Transcripts:
- KRT83:ENST00000293670.3:c.1306T>C:p.(Ser436Pro)
- Pathogenicity Data:
- Best Score: 0.999
- Polyphen2: 0.999 (D)
- Mutation Taster: 0.562
- SIFT: 0.003 (D)
- Frequency Data:
- No frequency data
- Proximity score 0.500 in interactome to PRKRA and phenotypic similarity 0.629 to mouse mutant of PRKRA.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0030029, wide cranial sutures
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.747
Phenotype Score: 0.500
Variant Score: 0.999
- Transcripts:
- THAP12:ENST00000260045.3:c.1828T>G:p.(Ser610Ala)
- Pathogenicity Data:
- Best Score: 0.998991
- Polyphen2: 0.004 (B)
- Mutation Taster: 0.999 (P)
- SIFT: 0.539 (T)
- Frequency Data:
- TOPMed: 0.0008%
- gnomAD_E_NFE: 0.0010%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.745
Phenotype Score: 0.500
Variant Score: 0.997
- Transcripts:
- THAP12:ENST00000260045.3:c.1828T>G:p.(Ser610Ala)
- Pathogenicity Data:
- Best Score: 0.998991
- Polyphen2: 0.004 (B)
- Mutation Taster: 0.999 (P)
- SIFT: 0.539 (T)
- Frequency Data:
- TOPMed: 0.0008%
- gnomAD_E_NFE: 0.0010%
- Transcripts:
- THAP12:ENST00000260045.3:c.1674A>T:p.(Arg558Ser)
- Pathogenicity Data:
- Best Score: 0.996463
- Polyphen2: 0.295 (B)
- Mutation Taster: 0.996 (P)
- SIFT: 0.017 (D)
- Frequency Data:
- gnomAD_E_AMR: 0.0038%
- Phenotypic similarity 0.317 to mouse mutant involving ARHGAP25.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0002092, abnormal eye morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.502 in interactome to FGD1 and phenotypic similarity 0.621 to Mental retardation, X-linked syndromic 16 associated with FGD1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009466, Radial deviation of finger
- HP:0010055, Broad hallux - HP:0030084, Clinodactyly
- Proximity score 0.502 in interactome to FGD1 and phenotypic similarity 0.272 to mouse mutant of FGD1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001297, microphthalmia
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.747
Phenotype Score: 0.502
Variant Score: 0.997
- Transcripts:
- ARHGAP25:ENST00000295381.3:c.1513G>T:p.(Val505Phe)
- ARHGAP25:ENST00000409030.3:c.1492G>T:p.(Val498Phe)
- ARHGAP25:ENST00000409202.3:c.1516G>T:p.(Val506Phe)
- ARHGAP25:ENST00000409220.1:c.1495G>T:p.(Val499Phe)
- ARHGAP25:ENST00000467265.1:c.1396G>T:p.(Val466Phe)
- ARHGAP25:ENST00000479844.1:c.595G>T:p.(Val199Phe)
- Pathogenicity Data:
- Best Score: 0.999709
- Polyphen2: 0.541 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.002 (D)
- Frequency Data:
- ExAC EAS: 0.0232%
- gnomAD_E_EAS: 0.0232%
- Proximity score 0.501 in interactome to YY1 and phenotypic similarity 0.751 to Gabriele-de Vries syndrome associated with YY1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001822, Hallux valgus
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0006094, Finger joint hypermobility
- HP:0010055, Broad hallux - HP:0001822, Hallux valgus
- Known diseases:
- OMIM:110800 Adult i phenotype without cataract - autosomal dominant
- OMIM:116700 Cataract 13 with adult i phenotype - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.746
Phenotype Score: 0.501
Variant Score: 0.997
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.463 (P)
- Mutation Taster: 1.000 (P)
- Frequency Data:
- TOPMed: 0.0008%
- ExAC SAS: 0.0121%
- gnomAD_E_SAS: 0.0195%
- gnomAD_G_NFE: 0.0067%
- Proximity score 0.501 in interactome to GNAS and phenotypic similarity 0.784 to Pseudohypoparathyroidism type 1A associated with GNAS.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0002684, Thickened calvaria
- HP:0011304, Broad thumb - HP:0009642, Broad distal phalanx of the thumb
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Proximity score 0.501 in interactome to GNAS and phenotypic similarity 0.497 to mouse mutant of GNAS.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0003109, short femur
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb - MP:0003109, short femur
- HP:0010055, Broad hallux - MP:0003109, short femur
AUTOSOMAL_DOMINANT
Exomiser Score: 0.746
Phenotype Score: 0.501
Variant Score: 0.997
- Pathogenicity Data:
- Best Score: 0.999621
- Polyphen2: 0.899 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.177 (T)
- Frequency Data:
- TOPMed: 0.0008%
- ExAC NFE: 0.0060%
- gnomAD_E_NFE: 0.0054%
- gnomAD_E_OTH: 0.0182%
- gnomAD_G_NFE: 0.0067%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.044
Phenotype Score: 0.501
Variant Score: 0.544
- Pathogenicity Data:
- Best Score: 0.999621
- Polyphen2: 0.899 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.177 (T)
- Frequency Data:
- TOPMed: 0.0008%
- ExAC NFE: 0.0060%
- gnomAD_E_NFE: 0.0054%
- gnomAD_E_OTH: 0.0182%
- gnomAD_G_NFE: 0.0067%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0799%
- TOPMed: 0.0189%
- ExAC AMR: 0.0087%
- ExAC EAS: 0.5389%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_EAS: 0.4948%
- gnomAD_G_EAS: 0.3083%
- Proximity score 0.501 in interactome to GNAS and phenotypic similarity 0.784 to Pseudohypoparathyroidism type 1A associated with GNAS.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0002684, Thickened calvaria
- HP:0011304, Broad thumb - HP:0009642, Broad distal phalanx of the thumb
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Proximity score 0.501 in interactome to GNAS and phenotypic similarity 0.497 to mouse mutant of GNAS.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0003109, short femur
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb - MP:0003109, short femur
- HP:0010055, Broad hallux - MP:0003109, short femur
AUTOSOMAL_DOMINANT
Exomiser Score: 0.746
Phenotype Score: 0.501
Variant Score: 0.997
- Pathogenicity Data:
- Best Score: 0.999853
- Polyphen2: 0.368 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.140 (T)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0200%
- ExAC EAS: 0.0116%
- gnomAD_E_EAS: 0.0058%
- Phenotypic similarity 0.296 to mouse mutant involving SCAMP2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001304, cataract
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.500 in interactome to ANKH and phenotypic similarity 0.389 to Craniometaphyseal dysplasia associated with ANKH.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0004975, Erlenmeyer flask deformity of the femurs
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0004975, Erlenmeyer flask deformity of the femurs
- HP:0010055, Broad hallux - HP:0004975, Erlenmeyer flask deformity of the femurs
- Proximity score 0.500 in interactome to ANKH and phenotypic similarity 0.698 to mouse mutant of ANKH.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis - MP:0002932, abnormal joint morphology
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.746
Phenotype Score: 0.500
Variant Score: 0.998
- Transcripts:
- SCAMP2:ENST00000268099.9:c.416C>G:p.(Thr139Arg)
- Pathogenicity Data:
- Best Score: 0.998
- Polyphen2: 0.251 (B)
- SIFT: 0.002 (D)
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.498 to mouse mutant involving GGT3P.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0006396, decreased long bone epiphyseal plate size
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0003109, short femur
- HP:0010055, Broad hallux - MP:0003109, short femur
AUTOSOMAL_DOMINANT
Exomiser Score: 0.745
Phenotype Score: 0.498
Variant Score: 1.000
- Transcripts:
- GGT3P:ENST00000412448.1:n.1185+1del:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.745
Phenotype Score: 0.498
Variant Score: 1.000
- Transcripts:
- GGT3P:ENST00000412448.1:n.1185+1del:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- GGT3P:ENST00000412448.1:n.1027+2T>C:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- GGT3P:ENST00000412448.1:n.1186-5T>C:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- GGT3P:ENST00000412448.1:n.1186-7A>G:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- GGT3P:ENST00000412448.1:n.1184T>C:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.501 in interactome to PTPN11 and phenotypic similarity 0.656 to Noonan syndrome 1 associated with PTPN11.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009466, Radial deviation of finger
- HP:0010055, Broad hallux - HP:0030084, Clinodactyly
- Proximity score 0.501 in interactome to PTPN11 and phenotypic similarity 0.540 to mouse mutant of PTPN11.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0012514, pectus excavatum
- HP:0001363, Craniosynostosis - MP:0010031, abnormal cranium size
- HP:0011304, Broad thumb - MP:0012514, pectus excavatum
- HP:0010055, Broad hallux - MP:0012514, pectus excavatum
AUTOSOMAL_DOMINANT
Exomiser Score: 0.745
Phenotype Score: 0.501
Variant Score: 0.997
- Transcripts:
- KIR2DL1:ENST00000291633.7:c.229C>A:p.(His77Asn)
- KIR2DL1:ENST00000336077.6:c.229C>A:p.(His77Asn)
- KIR2DL1:ENST00000402254.2:c.35-44046C>A:p.(=)
- KIR2DL1:ENST00000538269.1:c.35-44046C>A:p.(=)
- KIR2DL1:ENST00000541392.1:c.35-44046C>A:p.(=)
- KIR2DL1:ENST00000396284.2:c.35-30403C>A:p.(=)
- KIR2DL1:ENST00000434419.2:c.716-9431C>A:p.(=)
- Pathogenicity Data:
- Best Score: 0.999
- Polyphen2: 0.710 (P)
- SIFT: 0.001 (D)
- Frequency Data:
- ExAC AFR: 0.0098%
- ExAC NFE: 0.0016%
- gnomAD_E_AFR: 0.0066%
- gnomAD_E_NFE: 0.0028%
- gnomAD_G_AFR: 0.0131%
- gnomAD_G_NFE: 0.0077%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.744
Phenotype Score: 0.501
Variant Score: 0.997
- Transcripts:
- KIR2DL1:ENST00000291633.7:c.229C>A:p.(His77Asn)
- KIR2DL1:ENST00000336077.6:c.229C>A:p.(His77Asn)
- KIR2DL1:ENST00000402254.2:c.35-44046C>A:p.(=)
- KIR2DL1:ENST00000538269.1:c.35-44046C>A:p.(=)
- KIR2DL1:ENST00000541392.1:c.35-44046C>A:p.(=)
- KIR2DL1:ENST00000396284.2:c.35-30403C>A:p.(=)
- KIR2DL1:ENST00000434419.2:c.716-9431C>A:p.(=)
- Pathogenicity Data:
- Best Score: 0.999
- Polyphen2: 0.710 (P)
- SIFT: 0.001 (D)
- Frequency Data:
- ExAC AFR: 0.0098%
- ExAC NFE: 0.0016%
- gnomAD_E_AFR: 0.0066%
- gnomAD_E_NFE: 0.0028%
- gnomAD_G_AFR: 0.0131%
- gnomAD_G_NFE: 0.0077%
- Transcripts:
- KIR2DL1:ENST00000291633.7:c.230A>T:p.(His77Leu)
- KIR2DL1:ENST00000336077.6:c.230A>T:p.(His77Leu)
- KIR2DL1:ENST00000402254.2:c.35-44045A>T:p.(=)
- KIR2DL1:ENST00000538269.1:c.35-44045A>T:p.(=)
- KIR2DL1:ENST00000541392.1:c.35-44045A>T:p.(=)
- KIR2DL1:ENST00000396284.2:c.35-30402A>T:p.(=)
- KIR2DL1:ENST00000434419.2:c.716-9430A>T:p.(=)
- Pathogenicity Data:
- Best Score: 0.998
- Polyphen2: 0.147 (B)
- SIFT: 0.002 (D)
- Frequency Data:
- ExAC AFR: 0.0098%
- ExAC NFE: 0.0016%
- gnomAD_E_AFR: 0.0066%
- gnomAD_E_NFE: 0.0028%
- gnomAD_G_AFR: 0.0131%
- gnomAD_G_NFE: 0.0077%
- Transcripts:
- KIR2DL1:ENST00000291633.7:c.248C>G:p.(Ala83Gly)
- KIR2DL1:ENST00000336077.6:c.248C>G:p.(Ala83Gly)
- KIR2DL1:ENST00000402254.2:c.35-44027C>G:p.(=)
- KIR2DL1:ENST00000538269.1:c.35-44027C>G:p.(=)
- KIR2DL1:ENST00000541392.1:c.35-44027C>G:p.(=)
- KIR2DL1:ENST00000396284.2:c.35-30384C>G:p.(=)
- KIR2DL1:ENST00000434419.2:c.716-9412C>G:p.(=)
- Pathogenicity Data:
- Best Score: 0.955
- Polyphen2: 0.330 (B)
- SIFT: 0.045 (D)
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL1:ENST00000291633.7:c.202G>C:p.(Asp68His)
- KIR2DL1:ENST00000336077.6:c.202G>C:p.(Asp68His)
- KIR2DL1:ENST00000402254.2:c.35-44073G>C:p.(=)
- KIR2DL1:ENST00000538269.1:c.35-44073G>C:p.(=)
- KIR2DL1:ENST00000541392.1:c.35-44073G>C:p.(=)
- KIR2DL1:ENST00000396284.2:c.35-30430G>C:p.(=)
- KIR2DL1:ENST00000434419.2:c.716-9458G>C:p.(=)
- Pathogenicity Data:
- Best Score: 0.945
- Polyphen2: 0.198 (B)
- SIFT: 0.055 (D)
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL1:ENST00000291633.7:c.272C>A:p.(Thr91Lys)
- KIR2DL1:ENST00000336077.6:c.272C>A:p.(Thr91Lys)
- KIR2DL1:ENST00000402254.2:c.35-44003C>A:p.(=)
- KIR2DL1:ENST00000538269.1:c.35-44003C>A:p.(=)
- KIR2DL1:ENST00000541392.1:c.35-44003C>A:p.(=)
- KIR2DL1:ENST00000396284.2:c.35-30360C>A:p.(=)
- KIR2DL1:ENST00000434419.2:c.716-9388C>A:p.(=)
- Pathogenicity Data:
- Best Score: 0.921
- Polyphen2: 0.841 (P)
- SIFT: 0.079 (T)
- Frequency Data:
- ExAC AFR: 0.0392%
- ExAC NFE: 0.0015%
- gnomAD_E_AFR: 0.0466%
- gnomAD_E_NFE: 0.0018%
- Transcripts:
- KIR2DL1:ENST00000291633.7:c.550G>A:p.(Asp184Asn)
- KIR2DL1:ENST00000336077.6:c.550G>A:p.(Asp184Asn)
- KIR2DL1:ENST00000402254.2:c.35-42193G>A:p.(=)
- KIR2DL1:ENST00000538269.1:c.35-42193G>A:p.(=)
- KIR2DL1:ENST00000541392.1:c.35-42193G>A:p.(=)
- KIR2DL1:ENST00000396284.2:c.35-28550G>A:p.(=)
- KIR2DL1:ENST00000434419.2:c.716-7578G>A:p.(=)
- Pathogenicity Data:
- Best Score: 0.878
- Polyphen2: 0.014 (B)
- SIFT: 0.122 (T)
- Frequency Data:
- 1000Genomes: 0.0399%
- TOPMed: 0.0399%
- ExAC SAS: 0.0073%
- Transcripts:
- KIR2DL1:ENST00000291633.7:c.563G>A:p.(Gly188Asp)
- KIR2DL1:ENST00000336077.6:c.563G>A:p.(Gly188Asp)
- KIR2DL1:ENST00000402254.2:c.35-42180G>A:p.(=)
- KIR2DL1:ENST00000538269.1:c.35-42180G>A:p.(=)
- KIR2DL1:ENST00000541392.1:c.35-42180G>A:p.(=)
- KIR2DL1:ENST00000396284.2:c.35-28537G>A:p.(=)
- KIR2DL1:ENST00000434419.2:c.716-7565G>A:p.(=)
- Pathogenicity Data:
- Best Score: 0.949
- Polyphen2: 0.369 (B)
- SIFT: 0.051 (D)
- Frequency Data:
- 1000Genomes: 0.4992%
- TOPMed: 0.4992%
- gnomAD_E_AFR: 0.0793%
- gnomAD_E_AMR: 0.0032%
- gnomAD_G_AFR: 0.0141%
- Transcripts:
- KIR2DL1:ENST00000291633.7:c.709A>G:p.(Lys237Glu)
- KIR2DL1:ENST00000336077.6:c.709A>G:p.(Lys237Glu)
- KIR2DL1:ENST00000402254.2:c.35-38881A>G:p.(=)
- KIR2DL1:ENST00000538269.1:c.35-38881A>G:p.(=)
- KIR2DL1:ENST00000541392.1:c.35-38881A>G:p.(=)
- KIR2DL1:ENST00000396284.2:c.35-25238A>G:p.(=)
- KIR2DL1:ENST00000434419.2:c.716-4266A>G:p.(=)
- Pathogenicity Data:
- Best Score: 0.865
- Polyphen2: 0.010 (B)
- SIFT: 0.135 (T)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0200%
- gnomAD_E_AMR: 0.0064%
- gnomAD_E_EAS: 0.0710%
- gnomAD_E_FIN: 0.0048%
- gnomAD_E_NFE: 0.0030%
- gnomAD_E_SAS: 0.0120%
- gnomAD_G_EAS: 0.1928%
- Transcripts:
- KIR2DL1:ENST00000291633.7:c.523C>A:p.(Pro175Thr)
- KIR2DL1:ENST00000336077.6:c.523C>A:p.(Pro175Thr)
- KIR2DL1:ENST00000402254.2:c.35-42220C>A:p.(=)
- KIR2DL1:ENST00000538269.1:c.35-42220C>A:p.(=)
- KIR2DL1:ENST00000541392.1:c.35-42220C>A:p.(=)
- KIR2DL1:ENST00000396284.2:c.35-28577C>A:p.(=)
- KIR2DL1:ENST00000434419.2:c.716-7605C>A:p.(=)
- Pathogenicity Data:
- Best Score: 0.86300004
- Polyphen2: 0.002 (B)
- SIFT: 0.137 (T)
- Frequency Data:
- ESP AA: 0.0239%
- ESP All: 0.0081%
- gnomAD_E_AMR: 0.0257%
- gnomAD_E_EAS: 0.0059%
- gnomAD_E_NFE: 0.0049%
- gnomAD_E_OTH: 0.0206%
- gnomAD_E_SAS: 0.0159%
- gnomAD_G_AFR: 0.0142%
- gnomAD_G_AMR: 0.2653%
- Transcripts:
- KIR2DL1:ENST00000291633.7:c.535G>A:p.(Gly179Arg)
- KIR2DL1:ENST00000336077.6:c.535G>A:p.(Gly179Arg)
- KIR2DL1:ENST00000402254.2:c.35-42208G>A:p.(=)
- KIR2DL1:ENST00000538269.1:c.35-42208G>A:p.(=)
- KIR2DL1:ENST00000541392.1:c.35-42208G>A:p.(=)
- KIR2DL1:ENST00000396284.2:c.35-28565G>A:p.(=)
- KIR2DL1:ENST00000434419.2:c.716-7593G>A:p.(=)
- Pathogenicity Data:
- Best Score: 0.601
- Polyphen2: 0.274 (B)
- SIFT: 0.399 (T)
- Frequency Data:
- 1000Genomes: 0.0399%
- TOPMed: 0.0399%
- ESP EA: 0.0241%
- ESP All: 0.0159%
- gnomAD_E_AFR: 0.0074%
- gnomAD_E_AMR: 0.0064%
- gnomAD_E_NFE: 0.0010%
- gnomAD_E_SAS: 0.0279%
- gnomAD_G_AFR: 0.0141%
- Transcripts:
- KIR2DL1:ENST00000291633.7:c.331G>T:p.(Val111Leu)
- KIR2DL1:ENST00000336077.6:c.331G>T:p.(Val111Leu)
- KIR2DL1:ENST00000402254.2:c.35-43944G>T:p.(=)
- KIR2DL1:ENST00000538269.1:c.35-43944G>T:p.(=)
- KIR2DL1:ENST00000541392.1:c.35-43944G>T:p.(=)
- KIR2DL1:ENST00000396284.2:c.35-30301G>T:p.(=)
- KIR2DL1:ENST00000434419.2:c.716-9329G>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0532%
- gnomAD_E_AMR: 0.0031%
- gnomAD_E_NFE: 0.0075%
- gnomAD_E_SAS: 0.0067%
- gnomAD_G_AFR: 0.0749%
- gnomAD_G_FIN: 0.0597%
- gnomAD_G_NFE: 0.0219%
- Transcripts:
- KIR2DL1:ENST00000291633.7:c.608A>G:p.(His203Arg)
- KIR2DL1:ENST00000336077.6:c.608A>G:p.(His203Arg)
- KIR2DL1:ENST00000402254.2:c.35-42135A>G:p.(=)
- KIR2DL1:ENST00000538269.1:c.35-42135A>G:p.(=)
- KIR2DL1:ENST00000541392.1:c.35-42135A>G:p.(=)
- KIR2DL1:ENST00000396284.2:c.35-28492A>G:p.(=)
- KIR2DL1:ENST00000434419.2:c.716-7520A>G:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0799%
- TOPMed: 0.0799%
- gnomAD_E_AFR: 0.0707%
- gnomAD_E_AMR: 0.0127%
- gnomAD_E_NFE: 0.0047%
- gnomAD_G_AFR: 0.1781%
- gnomAD_G_NFE: 0.0226%
- Transcripts:
- KIR2DL1:ENST00000291633.7:c.262A>G:p.(Ser88Gly)
- KIR2DL1:ENST00000336077.6:c.262A>G:p.(Ser88Gly)
- KIR2DL1:ENST00000402254.2:c.35-44013A>G:p.(=)
- KIR2DL1:ENST00000538269.1:c.35-44013A>G:p.(=)
- KIR2DL1:ENST00000541392.1:c.35-44013A>G:p.(=)
- KIR2DL1:ENST00000396284.2:c.35-30370A>G:p.(=)
- KIR2DL1:ENST00000434419.2:c.716-9398A>G:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0799%
- ExAC AFR: 0.1371%
- ExAC AMR: 0.0355%
- ExAC EAS: 0.1868%
- ExAC FIN: 0.0312%
- ExAC NFE: 0.1022%
- ExAC OTH: 0.1147%
- gnomAD_E_AFR: 0.0998%
- gnomAD_E_AMR: 0.0370%
- gnomAD_E_EAS: 0.1348%
- gnomAD_E_FIN: 0.0092%
- gnomAD_E_NFE: 0.1480%
- gnomAD_E_OTH: 0.0566%
- gnomAD_G_AFR: 0.0249%
- gnomAD_G_EAS: 0.1913%
- gnomAD_G_NFE: 0.1622%
- Transcripts:
- KIR2DL1:ENST00000291633.7:c.529_530insCA:p.(Val177Alafs*75)
- KIR2DL1:ENST00000336077.6:c.529_530insCA:p.(Val177Alafs*72)
- KIR2DL1:ENST00000402254.2:c.35-42214_35-42213insCA:p.(=)
- KIR2DL1:ENST00000538269.1:c.35-42214_35-42213insCA:p.(=)
- KIR2DL1:ENST00000541392.1:c.35-42214_35-42213insCA:p.(=)
- KIR2DL1:ENST00000396284.2:c.35-28571_35-28570insCA:p.(=)
- KIR2DL1:ENST00000434419.2:c.716-7599_716-7598insCA:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 1.1725%
- gnomAD_E_AMR: 0.6766%
- gnomAD_E_EAS: 0.6586%
- gnomAD_E_FIN: 1.7201%
- gnomAD_E_NFE: 0.1655%
- gnomAD_E_OTH: 0.3689%
- gnomAD_E_SAS: 0.2002%
- gnomAD_G_AFR: 0.1202%
- gnomAD_G_AMR: 0.2778%
- gnomAD_G_EAS: 0.2019%
- gnomAD_G_FIN: 0.0323%
- gnomAD_G_NFE: 0.1043%
- gnomAD_G_OTH: 0.1190%
- Transcripts:
- KIR2DL1:ENST00000291633.7:c.527_528del:p.(Lys176Serfs*8)
- KIR2DL1:ENST00000336077.6:c.527_528del:p.(Lys176Serfs*8)
- KIR2DL1:ENST00000402254.2:c.35-42216_35-42215del:p.(=)
- KIR2DL1:ENST00000538269.1:c.35-42216_35-42215del:p.(=)
- KIR2DL1:ENST00000541392.1:c.35-42216_35-42215del:p.(=)
- KIR2DL1:ENST00000396284.2:c.35-28573_35-28572del:p.(=)
- KIR2DL1:ENST00000434419.2:c.716-7601_716-7600del:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 1.1449%
- gnomAD_E_AMR: 0.6713%
- gnomAD_E_EAS: 0.6555%
- gnomAD_E_FIN: 1.7296%
- gnomAD_E_NFE: 0.1753%
- gnomAD_E_OTH: 0.4076%
- gnomAD_E_SAS: 0.1871%
- gnomAD_G_AFR: 0.1155%
- gnomAD_G_AMR: 0.1362%
- gnomAD_G_EAS: 0.1948%
- gnomAD_G_FIN: 0.0319%
- gnomAD_G_NFE: 0.0868%
- gnomAD_G_OTH: 0.1157%
- Transcripts:
- KIR2DL1:ENST00000291633.7:c.419T>A:p.(Leu140Gln)
- KIR2DL1:ENST00000336077.6:c.419T>A:p.(Leu140Gln)
- KIR2DL1:ENST00000402254.2:c.35-42324T>A:p.(=)
- KIR2DL1:ENST00000538269.1:c.35-42324T>A:p.(=)
- KIR2DL1:ENST00000541392.1:c.35-42324T>A:p.(=)
- KIR2DL1:ENST00000396284.2:c.35-28681T>A:p.(=)
- KIR2DL1:ENST00000434419.2:c.716-7709T>A:p.(=)
- Pathogenicity Data:
- Best Score: 0.39999998
- Polyphen2: 0.001 (B)
- SIFT: 0.600 (T)
- Frequency Data:
- gnomAD_E_AFR: 0.0234%
- gnomAD_E_AMR: 0.0472%
- gnomAD_E_EAS: 0.0305%
- gnomAD_E_FIN: 0.9915%
- gnomAD_E_NFE: 0.0275%
- gnomAD_E_OTH: 0.1511%
- gnomAD_E_SAS: 0.0124%
- gnomAD_G_AFR: 0.0315%
- gnomAD_G_EAS: 0.0684%
- gnomAD_G_FIN: 0.0339%
- gnomAD_G_NFE: 0.0269%
- Transcripts:
- KIR2DL1:ENST00000291633.7:c.194T>C:p.(Met65Thr)
- KIR2DL1:ENST00000336077.6:c.194T>C:p.(Met65Thr)
- KIR2DL1:ENST00000402254.2:c.35-44081T>C:p.(=)
- KIR2DL1:ENST00000538269.1:c.35-44081T>C:p.(=)
- KIR2DL1:ENST00000541392.1:c.35-44081T>C:p.(=)
- KIR2DL1:ENST00000396284.2:c.35-30438T>C:p.(=)
- KIR2DL1:ENST00000434419.2:c.716-9466T>C:p.(=)
- Pathogenicity Data:
- Best Score: 0.22000003
- SIFT: 0.780 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL1:ENST00000291633.7:c.339T>G:p.(=)
- KIR2DL1:ENST00000336077.6:c.339T>G:p.(=)
- KIR2DL1:ENST00000402254.2:c.35-43936T>G:p.(=)
- KIR2DL1:ENST00000538269.1:c.35-43936T>G:p.(=)
- KIR2DL1:ENST00000541392.1:c.35-43936T>G:p.(=)
- KIR2DL1:ENST00000396284.2:c.35-30293T>G:p.(=)
- KIR2DL1:ENST00000434419.2:c.716-9321T>G:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL1:ENST00000291633.7:c.225A>G:p.(=)
- KIR2DL1:ENST00000336077.6:c.225A>G:p.(=)
- KIR2DL1:ENST00000402254.2:c.35-44050A>G:p.(=)
- KIR2DL1:ENST00000538269.1:c.35-44050A>G:p.(=)
- KIR2DL1:ENST00000541392.1:c.35-44050A>G:p.(=)
- KIR2DL1:ENST00000396284.2:c.35-30407A>G:p.(=)
- KIR2DL1:ENST00000434419.2:c.716-9435A>G:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0465%
- gnomAD_E_AMR: 0.0062%
- gnomAD_E_FIN: 0.0046%
- gnomAD_E_NFE: 0.0037%
- gnomAD_E_SAS: 0.0034%
- gnomAD_G_AFR: 0.0133%
- gnomAD_G_NFE: 0.0078%
- Transcripts:
- KIR2DL1:ENST00000291633.7:c.576C>T:p.(=)
- KIR2DL1:ENST00000336077.6:c.576C>T:p.(=)
- KIR2DL1:ENST00000402254.2:c.35-42167C>T:p.(=)
- KIR2DL1:ENST00000538269.1:c.35-42167C>T:p.(=)
- KIR2DL1:ENST00000541392.1:c.35-42167C>T:p.(=)
- KIR2DL1:ENST00000396284.2:c.35-28524C>T:p.(=)
- KIR2DL1:ENST00000434419.2:c.716-7552C>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC EAS: 0.0118%
- ExAC NFE: 0.0016%
- ExAC SAS: 0.0206%
- gnomAD_E_EAS: 0.0062%
- gnomAD_E_NFE: 0.0011%
- gnomAD_E_SAS: 0.0588%
- Transcripts:
- KIR2DL1:ENST00000291633.7:c.273G>A:p.(=)
- KIR2DL1:ENST00000336077.6:c.273G>A:p.(=)
- KIR2DL1:ENST00000402254.2:c.35-44002G>A:p.(=)
- KIR2DL1:ENST00000538269.1:c.35-44002G>A:p.(=)
- KIR2DL1:ENST00000541392.1:c.35-44002G>A:p.(=)
- KIR2DL1:ENST00000396284.2:c.35-30359G>A:p.(=)
- KIR2DL1:ENST00000434419.2:c.716-9387G>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0399%
- TOPMed: 0.0399%
- ExAC AFR: 0.0293%
- ExAC AMR: 0.0178%
- ExAC EAS: 0.0233%
- ExAC NFE: 0.0046%
- ExAC SAS: 0.0939%
- gnomAD_E_AFR: 0.0199%
- gnomAD_E_AMR: 0.0092%
- gnomAD_E_EAS: 0.0117%
- gnomAD_E_NFE: 0.0065%
- gnomAD_E_SAS: 0.0907%
- gnomAD_G_AFR: 0.0617%
- gnomAD_G_NFE: 0.0219%
- Transcripts:
- KIR2DL1:ENST00000291633.7:c.368T>C:p.(Ile123Thr)
- KIR2DL1:ENST00000336077.6:c.368T>C:p.(Ile123Thr)
- KIR2DL1:ENST00000402254.2:c.35-43907T>C:p.(=)
- KIR2DL1:ENST00000538269.1:c.35-43907T>C:p.(=)
- KIR2DL1:ENST00000541392.1:c.35-43907T>C:p.(=)
- KIR2DL1:ENST00000396284.2:c.35-30264T>C:p.(=)
- KIR2DL1:ENST00000434419.2:c.716-9292T>C:p.(=)
- Pathogenicity Data:
- Best Score: 0.001
- Polyphen2: 0.001 (B)
- Frequency Data:
- 1000Genomes: 0.0399%
- TOPMed: 0.0399%
- gnomAD_E_AFR: 0.0202%
- gnomAD_E_AMR: 0.0159%
- gnomAD_G_AFR: 0.0399%
- Proximity score 0.505 in interactome to COL10A1 and phenotypic similarity 0.658 to Metaphyseal chondrodysplasia, Schmid type associated with COL10A1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0005819, Short middle phalanx of finger
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009844, Broad middle phalanx of finger
- HP:0010055, Broad hallux - HP:0009844, Broad middle phalanx of finger
- Proximity score 0.505 in interactome to COL10A1 and phenotypic similarity 0.579 to mouse mutant of COL10A1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0004509, abnormal pelvic girdle bone morphology
- HP:0001363, Craniosynostosis - MP:0008272, abnormal endochondral bone ossification
- HP:0011304, Broad thumb - MP:0004509, abnormal pelvic girdle bone morphology
- HP:0010055, Broad hallux - MP:0004509, abnormal pelvic girdle bone morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.745
Phenotype Score: 0.505
Variant Score: 0.991
- Pathogenicity Data:
- Best Score: 0.999879
- Polyphen2: 0.990 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.002 (D)
- Frequency Data:
- TOPMed: 0.0096%
- ESP AA: 0.0454%
- ESP All: 0.0154%
- ExAC AFR: 0.0192%
- ExAC AMR: 0.0086%
- ExAC EAS: 0.0231%
- ExAC NFE: 0.0030%
- ExAC SAS: 0.0182%
- gnomAD_E_AFR: 0.0131%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_EAS: 0.0290%
- gnomAD_E_NFE: 0.0027%
- gnomAD_E_SAS: 0.0097%
- gnomAD_G_EAS: 0.0617%
- gnomAD_G_NFE: 0.0067%
- Proximity score 0.502 in interactome to TAF6 and phenotypic similarity 0.812 to Alazami-Yuan syndrome associated with TAF6.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010055, Broad hallux
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0010055, Broad hallux
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
- Proximity score 0.502 in interactome to TAF6 and phenotypic similarity 0.257 to mouse mutant of TAF6.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0011965, decreased total retina thickness
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.744
Phenotype Score: 0.502
Variant Score: 0.996
- Pathogenicity Data:
- Best Score: 0.998368
- Polyphen2: 0.594 (P)
- Mutation Taster: 0.998 (P)
- SIFT: 0.005 (D)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0064%
- ExAC SAS: 0.0132%
- gnomAD_E_AFR: 0.0131%
- gnomAD_E_EAS: 0.0098%
- gnomAD_E_FIN: 0.0133%
- gnomAD_E_NFE: 0.0018%
- gnomAD_E_SAS: 0.0088%
- Proximity score 0.503 in interactome to PTH1R and phenotypic similarity 0.688 to Eiken syndrome associated with PTH1R.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0009371, Type A1 brachydactyly
- HP:0001363, Craniosynostosis - HP:0002684, Thickened calvaria
- HP:0011304, Broad thumb - HP:0001783, Broad metatarsal
- HP:0010055, Broad hallux - HP:0001847, Long hallux
- Proximity score 0.503 in interactome to PTH1R and phenotypic similarity 0.589 to mouse mutant of PTH1R.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0003662, abnormal long bone epiphyseal plate proliferative zone
- HP:0001363, Craniosynostosis - MP:0000440, domed cranium
- HP:0011304, Broad thumb - MP:0003662, abnormal long bone epiphyseal plate proliferative zone
- HP:0010055, Broad hallux - MP:0003662, abnormal long bone epiphyseal plate proliferative zone
AUTOSOMAL_DOMINANT
Exomiser Score: 0.744
Phenotype Score: 0.503
Variant Score: 0.994
- Transcripts:
- GIP:ENST00000357424.2:c.181T>C:p.(Tyr61His)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.999 (D)
- Mutation Taster: 0.978 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- 1000Genomes: 0.0399%
- TOPMed: 0.0023%
- ExAC EAS: 0.0347%
- gnomAD_E_EAS: 0.0232%
- Proximity score 0.500 in interactome to FGFRL1 and phenotypic similarity 0.778 to mouse mutant of FGFRL1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0004509, abnormal pelvic girdle bone morphology
- HP:0001363, Craniosynostosis - MP:0010743, delayed cranial suture closure
- HP:0011304, Broad thumb - MP:0012514, pectus excavatum
- HP:0010055, Broad hallux - MP:0004509, abnormal pelvic girdle bone morphology
- Proximity score 0.500 in interactome to FGFRL1 and phenotypic similarity 0.313 to fish mutant of FGFRL1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - ZP:0005133, palatoquadrate cartilage shape, abnormal
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.744
Phenotype Score: 0.500
Variant Score: 0.997
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.987 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0011%
- ExAC EAS: 0.0232%
- gnomAD_E_EAS: 0.0116%
- gnomAD_E_NFE: 0.0009%
- Proximity score 0.504 in interactome to RRAS2 and phenotypic similarity 0.642 to Noonan syndrome associated with RRAS2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0004209, Clinodactyly of the 5th finger
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Proximity score 0.504 in interactome to RRAS2 and phenotypic similarity 0.309 to mouse mutant of RRAS2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001326, retinal degeneration
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.744
Phenotype Score: 0.504
Variant Score: 0.992
- Transcripts:
- RASIP1:ENST00000222145.4:c.788T>G:p.(Leu263Arg)
- Pathogenicity Data:
- Best Score: 0.992
- Polyphen2: 0.638 (P)
- Mutation Taster: 0.953 (P)
- SIFT: 0.008 (D)
- Frequency Data:
- No frequency data
- Proximity score 0.500 in interactome to TNNI2 and phenotypic similarity 0.494 to Distal arthrogryposis type 1 associated with TNNI2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010557, Overlapping fingers
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001181, Adducted thumb
- HP:0010055, Broad hallux - HP:0010557, Overlapping fingers
- Proximity score 0.500 in interactome to TNNI2 and phenotypic similarity 0.611 to mouse mutant of TNNI2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0006395, abnormal epiphyseal plate morphology
- HP:0001363, Craniosynostosis - MP:0008273, abnormal intramembranous bone ossification
- HP:0011304, Broad thumb - MP:0004351, short humerus
- HP:0010055, Broad hallux - MP:0006395, abnormal epiphyseal plate morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.743
Phenotype Score: 0.500
Variant Score: 0.996
- Transcripts:
- TMOD4:ENST00000416280.2:c.766C>T:p.(Arg256*)
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- Frequency Data:
- TOPMed: 0.0030%
- UK10K: 0.0264%
- ExAC AFR: 0.0096%
- ExAC NFE: 0.0015%
- ExAC SAS: 0.0061%
- gnomAD_E_AFR: 0.0065%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_NFE: 0.0027%
- gnomAD_E_SAS: 0.0032%
- Phenotypic similarity 0.541 to X-linked non-syndromic intellectual disability associated with FRMPD4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0004691, 2-3 toe syndactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0006118, Shortening of all distal phalanges of the fingers
- HP:0010055, Broad hallux - HP:0004691, 2-3 toe syndactyly
- Phenotypic similarity 0.399 to mouse mutant involving FRMPD4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002764, short tibia
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002764, short tibia
- HP:0010055, Broad hallux - MP:0002764, short tibia
- Known diseases:
- OMIM:300983 Intellectual developmental disorder, X-linked 104 - X-linked recessive
- ORPHA:777 X-linked non-syndromic intellectual disability - X-linked recessive
X_RECESSIVE
Exomiser Score: 0.742
Phenotype Score: 0.541
Variant Score: 0.950
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.541 to ORPHA:777 X-linked non-syndromic intellectual disability
- Transcripts:
- FRMPD4:ENST00000380682.1:c.1636C>T:p.(Leu546Phe)
- Pathogenicity Data:
- Best Score: 0.964
- Polyphen2: 0.075 (B)
- SIFT: 0.036 (D)
- Frequency Data:
- 1000Genomes: 0.0795%
- TOPMed: 0.0060%
- ExAC EAS: 0.0611%
- gnomAD_E_EAS: 0.0806%
- gnomAD_G_EAS: 0.1041%
- Proximity score 0.500 in interactome to AHSG and phenotypic similarity 0.645 to Alopecia-intellectual disability syndrome associated with AHSG.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001156, Brachydactyly
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Proximity score 0.500 in interactome to AHSG and phenotypic similarity 0.399 to mouse mutant of AHSG.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002764, short tibia
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002764, short tibia
- HP:0010055, Broad hallux - MP:0002764, short tibia
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.741
Phenotype Score: 0.500
Variant Score: 0.995
- Transcripts:
- MUC17:ENST00000306151.4:c.2023G>T:p.(Gly675Cys)
- Pathogenicity Data:
- Best Score: 0.995
- Polyphen2: 0.129 (B)
- SIFT: 0.005 (D)
- Frequency Data:
- No frequency data
AUTOSOMAL_DOMINANT
Exomiser Score: 0.712
Phenotype Score: 0.500
Variant Score: 0.979
- Transcripts:
- MUC17:ENST00000306151.4:c.9725T>C:p.(Leu3242Pro)
- Pathogenicity Data:
- Best Score: 0.979
- Polyphen2: 0.979 (D)
- SIFT: 0.098 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- MUC17:ENST00000306151.4:c.2016T>C:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0129%
- ESP AA: 0.0227%
- ESP All: 0.0077%
- ExAC AFR: 0.0288%
- ExAC AMR: 0.0259%
- gnomAD_E_AFR: 0.0261%
- gnomAD_E_AMR: 0.0179%
- gnomAD_G_AFR: 0.0230%
- Proximity score 0.500 in interactome to TFPI and phenotypic similarity 0.614 to mouse mutant of TFPI.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000585, kinked tail
- HP:0001363, Craniosynostosis - MP:0000084, abnormal fontanelle morphology
- HP:0011304, Broad thumb - MP:0000585, kinked tail
- HP:0010055, Broad hallux - MP:0000585, kinked tail
- Known diseases:
- OMIM:612926 Hemolytic uremic syndrome, atypical, susceptibility to, 6 (susceptibility)
- OMIM:614486 Thrombophilia due to thrombomodulin defect - unknown
AUTOSOMAL_DOMINANT
Exomiser Score: 0.740
Phenotype Score: 0.500
Variant Score: 0.995
- Transcripts:
- THBD:ENST00000377103.2:c.1232C>T:p.(Thr411Ile)
- Pathogenicity Data:
- Best Score: 0.995
- Polyphen2: 0.592 (P)
- SIFT: 0.005 (D)
- Frequency Data:
- TOPMed: 0.0008%
- Proximity score 0.500 in interactome to HS2ST1 and phenotypic similarity 0.703 to Neurofacioskeletal syndrome with or without renal agenesis associated with HS2ST1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0011927, Short digit
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009836, Broad distal phalanx of finger
- HP:0010055, Broad hallux - HP:0010186, Broad distal phalanx of the toes
- Proximity score 0.500 in interactome to HS2ST1 and phenotypic similarity 0.698 to mouse mutant of HS2ST1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000562, polydactyly
- HP:0001363, Craniosynostosis - MP:0002896, abnormal bone mineralization
- HP:0011304, Broad thumb - MP:0000562, polydactyly
- HP:0010055, Broad hallux - MP:0000562, polydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.740
Phenotype Score: 0.500
Variant Score: 0.995
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.711 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.021 (D)
- Frequency Data:
- TOPMed: 0.0019%
- ExAC EAS: 0.0233%
- ExAC SAS: 0.0063%
- gnomAD_E_EAS: 0.0359%
- gnomAD_E_SAS: 0.0034%
- Proximity score 0.500 in interactome to SEC24C and phenotypic similarity 0.740 to 22q11.2 deletion syndrome associated with SEC24C.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001829, Foot polydactyly
- HP:0001363, Craniosynostosis - HP:0011324, Multiple suture craniosynostosis
- HP:0011304, Broad thumb - HP:0001161, Hand polydactyly
- HP:0010055, Broad hallux - HP:0001829, Foot polydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.740
Phenotype Score: 0.500
Variant Score: 0.995
- Transcripts:
- KIR3DL1:ENST00000402254.2:c.1089G>C:p.(Trp363Cys)
- Pathogenicity Data:
- Best Score: 0.995
- Polyphen2: 0.995 (D)
- SIFT: 0.011 (D)
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.738
Phenotype Score: 0.500
Variant Score: 0.994
- Transcripts:
- KIR3DL1:ENST00000402254.2:c.1089G>C:p.(Trp363Cys)
- Pathogenicity Data:
- Best Score: 0.995
- Polyphen2: 0.995 (D)
- SIFT: 0.011 (D)
- Frequency Data:
- No frequency data
- Transcripts:
- KIR3DL1:ENST00000402254.2:c.1066C>T:p.(Leu356Phe)
- Pathogenicity Data:
- Best Score: 0.993
- Polyphen2: 0.993 (D)
- SIFT: 0.630 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- KIR3DL1:ENST00000402254.2:c.1084C>T:p.(Arg362Cys)
- Pathogenicity Data:
- Best Score: 0.982
- Polyphen2: 0.724 (P)
- SIFT: 0.018 (D)
- Frequency Data:
- ExAC NFE: 0.0015%
- gnomAD_E_NFE: 0.0027%
- Transcripts:
- KIR3DL1:ENST00000326542.7:c.475G>T:p.(Gly159Trp)
- KIR3DL1:ENST00000358178.4:c.190G>T:p.(Gly64Trp)
- KIR3DL1:ENST00000391728.4:c.475G>T:p.(Gly159Trp)
- KIR3DL1:ENST00000402254.2:c.475G>T:p.(Gly159Trp)
- KIR3DL1:ENST00000538269.1:c.475G>T:p.(Gly159Trp)
- KIR3DL1:ENST00000541392.1:c.475G>T:p.(Gly159Trp)
- Pathogenicity Data:
- Best Score: 0.981
- Polyphen2: 0.651 (P)
- SIFT: 0.019 (D)
- Frequency Data:
- No frequency data
- Transcripts:
- KIR3DL1:ENST00000402254.2:c.1043T>C:p.(Val348Ala)
- Pathogenicity Data:
- Best Score: 0.966
- Polyphen2: 0.966 (D)
- SIFT: 0.105 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- KIR3DL1:ENST00000402254.2:c.1006T>C:p.(Cys336Arg)
- Pathogenicity Data:
- Best Score: 0.866
- SIFT: 0.134 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- KIR3DL1:ENST00000402254.2:c.1021G>A:p.(Val341Ile)
- Pathogenicity Data:
- Best Score: 0.848
- Polyphen2: 0.010 (B)
- SIFT: 0.152 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- KIR3DL1:ENST00000402254.2:c.1156C>G:p.(Gln386Glu)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- KIR3DL1:ENST00000402254.2:c.1060C>A:p.(Leu354Ile)
- Pathogenicity Data:
- Best Score: 0.491
- Polyphen2: 0.009 (B)
- SIFT: 0.509 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- KIR3DL1:ENST00000402254.2:c.1081T>C:p.(Tyr361His)
- Pathogenicity Data:
- Best Score: 0.004
- Polyphen2: 0.004 (B)
- Frequency Data:
- gnomAD_E_AMR: 0.0060%
- Transcripts:
- KIR3DL1:ENST00000402254.2:c.1048T>A:p.(Phe350Ile)
- Pathogenicity Data:
- Best Score: 0.001
- Polyphen2: 0.001 (B)
- Frequency Data:
- ExAC NFE: 0.0015%
- gnomAD_E_NFE: 0.0009%
- Proximity score 0.503 in interactome to CANT1 and phenotypic similarity 0.638 to Desbuquois dysplasia 1 associated with CANT1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009611, Bifid distal phalanx of the thumb
- HP:0010055, Broad hallux - HP:0010097, Partial duplication of the distal phalanx of the hallux
- Proximity score 0.503 in interactome to CANT1 and phenotypic similarity 0.315 to mouse mutant of CANT1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002111, abnormal tail morphology
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002111, abnormal tail morphology
- HP:0010055, Broad hallux - MP:0002111, abnormal tail morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.740
Phenotype Score: 0.503
Variant Score: 0.992
- Transcripts:
- PKM:ENST00000319622.6:c.1147C>T:p.(Arg383Cys)
- PKM:ENST00000389093.3:c.1147C>T:p.(Arg383Cys)
- PKM:ENST00000565154.1:c.1147C>T:p.(Arg383Cys)
- PKM:ENST00000565184.1:c.1147C>T:p.(Arg383Cys)
- PKM:ENST00000568459.1:c.1147C>T:p.(Arg383Cys)
- PKM:ENST00000568883.1:c.652C>T:p.(Arg218Cys)
- PKM:ENST00000335181.5:c.1141-562C>T:p.(=)
- PKM:ENST00000449901.2:c.1096-562C>T:p.(=)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.013 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.081 (T)
- Frequency Data:
- TOPMed: 0.0072%
- ExAC EAS: 0.0579%
- ExAC NFE: 0.0015%
- ExAC SAS: 0.0061%
- gnomAD_E_EAS: 0.0406%
- gnomAD_E_NFE: 0.0018%
- gnomAD_E_SAS: 0.0032%
- gnomAD_G_NFE: 0.0067%
- Proximity score 0.503 in interactome to LMBR1 and phenotypic similarity 0.714 to Triphalangeal thumb, type I associated with LMBR1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001830, Postaxial foot polydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0005866, Opposable triphalangeal thumb
- HP:0010055, Broad hallux - HP:0001841, Preaxial foot polydactyly
- Proximity score 0.503 in interactome to LMBR1 and phenotypic similarity 0.806 to mouse mutant of LMBR1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000564, syndactyly
- HP:0001363, Craniosynostosis - MP:0000554, abnormal carpal bone morphology
- HP:0011304, Broad thumb - MP:0002543, brachyphalangia
- HP:0010055, Broad hallux - MP:0000564, syndactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.739
Phenotype Score: 0.503
Variant Score: 0.991
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.356 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.132 (T)
- Frequency Data:
- TOPMed: 0.0015%
- ExAC EAS: 0.0347%
- gnomAD_E_EAS: 0.0524%
- gnomAD_G_EAS: 0.0617%
- Proximity score 0.506 in interactome to ASAP1 and phenotypic similarity 0.712 to mouse mutant of ASAP1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0005306, abnormal phalanx morphology
- HP:0001363, Craniosynostosis - MP:0003420, delayed intramembranous bone ossification
- HP:0011304, Broad thumb - MP:0005306, abnormal phalanx morphology
- HP:0010055, Broad hallux - MP:0005306, abnormal phalanx morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.738
Phenotype Score: 0.506
Variant Score: 0.987
- Transcripts:
- PTK2B:ENST00000338238.4:c.2399C>T:p.(Thr800Met)
- PTK2B:ENST00000346049.5:c.2525C>T:p.(Thr842Met)
- PTK2B:ENST00000397497.4:c.1637C>T:p.(Thr546Met)
- PTK2B:ENST00000397501.1:c.2525C>T:p.(Thr842Met)
- PTK2B:ENST00000420218.2:c.2399C>T:p.(Thr800Met)
- PTK2B:ENST00000517339.1:c.2399C>T:p.(Thr800Met)
- PTK2B:ENST00000544172.1:c.2525C>T:p.(Thr842Met)
- Pathogenicity Data:
- Best Score: 0.988593
- Polyphen2: 0.329 (B)
- Mutation Taster: 0.989 (P)
- SIFT: 0.125 (T)
- Frequency Data:
- TOPMed: 0.0023%
- ExAC EAS: 0.0116%
- ExAC NFE: 0.0030%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_EAS: 0.0058%
- gnomAD_E_NFE: 0.0009%
- Proximity score 0.500 in interactome to RAC3 and phenotypic similarity 0.624 to Neurodevelopmental disorder with structural brain anomalies and dysmorphic facies associated with RAC3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0030084, Clinodactyly
- HP:0001363, Craniosynostosis - HP:0011320, Unilambdoid synostosis
- HP:0011304, Broad thumb - HP:0030084, Clinodactyly
- HP:0010055, Broad hallux - HP:0030084, Clinodactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.737
Phenotype Score: 0.500
Variant Score: 0.993
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.946 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.012 (D)
- Frequency Data:
- TOPMed: 0.0026%
- ExAC EAS: 0.0116%
- ExAC SAS: 0.0303%
- gnomAD_E_EAS: 0.0058%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_SAS: 0.0520%
- Phenotypic similarity 0.305 to zebrafish mutant involving DDX18.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - ZP:0000407, head decreased width, abnormal
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.501 in interactome to BMS1 and phenotypic similarity 0.602 to Aplasia cutis congenita associated with BMS1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001770, Toe syndactyly
- HP:0001363, Craniosynostosis - HP:0001362, Calvarial skull defect
- HP:0011304, Broad thumb - HP:0006101, Finger syndactyly
- HP:0010055, Broad hallux - HP:0001770, Toe syndactyly
- Proximity score 0.501 in interactome to BMS1 and phenotypic similarity 0.299 to mouse mutant of BMS1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001303, abnormal lens morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.736
Phenotype Score: 0.501
Variant Score: 0.991
- Transcripts:
- DDX18:ENST00000263239.2:c.791C>T:p.(Ala264Val)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.345 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.001 (D)
- Frequency Data:
- gnomAD_G_EAS: 0.0617%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.044
Phenotype Score: 0.501
Variant Score: 0.545
- Transcripts:
- DDX18:ENST00000263239.2:c.791C>T:p.(Ala264Val)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.345 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.001 (D)
- Frequency Data:
- gnomAD_G_EAS: 0.0617%
- Transcripts:
- DDX18:ENST00000263239.2:c.1833G>C:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0004%
- ExAC EAS: 0.0231%
- ExAC NFE: 0.0030%
- gnomAD_E_EAS: 0.0175%
- gnomAD_E_NFE: 0.0018%
- gnomAD_G_EAS: 0.0617%
- Phenotypic similarity 0.318 to mouse mutant involving BAZ2B.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.500 in interactome to BPTF and phenotypic similarity 0.869 to Non-specific syndromic intellectual disability associated with BPTF.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010109, Short hallux
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0011304, Broad thumb
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
- Proximity score 0.500 in interactome to BPTF and phenotypic similarity 0.330 to mouse mutant of BPTF.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0004609, vertebral fusion
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.735
Phenotype Score: 0.500
Variant Score: 0.992
- Pathogenicity Data:
- Best Score: 0.993144
- Polyphen2: 0.306 (B)
- Mutation Taster: 0.993 (P)
- SIFT: 0.028 (D)
- Frequency Data:
- TOPMed: 0.0096%
- gnomAD_E_EAS: 0.0061%
- gnomAD_E_NFE: 0.0009%
- Proximity score 0.500 in interactome to TRIP13 and phenotypic similarity 0.446 to Mosaic variegated aneuploidy syndrome associated with TRIP13.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0004209, Clinodactyly of the 5th finger
- HP:0001363, Craniosynostosis - HP:0002007, Frontal bossing
- HP:0011304, Broad thumb - HP:0004209, Clinodactyly of the 5th finger
- HP:0010055, Broad hallux - HP:0004209, Clinodactyly of the 5th finger
- Proximity score 0.500 in interactome to TRIP13 and phenotypic similarity 0.695 to mouse mutant of TRIP13.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.734
Phenotype Score: 0.500
Variant Score: 0.991
- Pathogenicity Data:
- Best Score: 0.999999
- Polyphen2: 0.397 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.011 (D)
- Frequency Data:
- TOPMed: 0.0011%
- ExAC EAS: 0.0347%
- ExAC NFE: 0.0015%
- ExAC SAS: 0.0121%
- gnomAD_E_EAS: 0.0116%
- gnomAD_E_NFE: 0.0027%
- gnomAD_E_SAS: 0.0097%
- gnomAD_G_EAS: 0.0617%
- gnomAD_G_NFE: 0.0067%
- Proximity score 0.500 in interactome to AMMECR1 and phenotypic similarity 0.667 to Midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis associated with AMMECR1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0004209, Clinodactyly of the 5th finger
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009836, Broad distal phalanx of finger
- HP:0010055, Broad hallux - HP:0004209, Clinodactyly of the 5th finger
AUTOSOMAL_DOMINANT
Exomiser Score: 0.732
Phenotype Score: 0.500
Variant Score: 0.990
- Transcripts:
- PNLIPRP3:ENST00000369230.3:c.191C>T:p.(Pro64Leu)
- Pathogenicity Data:
- Best Score: 0.993
- Polyphen2: 0.128 (B)
- SIFT: 0.007 (D)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0015%
- ExAC EAS: 0.0116%
- gnomAD_E_EAS: 0.0237%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.198
Phenotype Score: 0.500
Variant Score: 0.728
- Transcripts:
- PNLIPRP3:ENST00000369230.3:c.191C>T:p.(Pro64Leu)
- Pathogenicity Data:
- Best Score: 0.993
- Polyphen2: 0.128 (B)
- SIFT: 0.007 (D)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0015%
- ExAC EAS: 0.0116%
- gnomAD_E_EAS: 0.0237%
- Transcripts:
- PNLIPRP3:ENST00000369230.3:c.986G>C:p.(Arg329Thr)
- Pathogenicity Data:
- Best Score: 0.923
- Polyphen2: 0.063 (B)
- SIFT: 0.077 (T)
- Frequency Data:
- 1000Genomes: 0.2596%
- TOPMed: 0.0612%
- UK10K: 0.0264%
- ESP AA: 0.0227%
- ESP EA: 0.0814%
- ESP All: 0.0615%
- ExAC AFR: 0.0097%
- ExAC EAS: 1.5390%
- ExAC FIN: 0.0455%
- ExAC NFE: 0.0330%
- ExAC OTH: 0.3319%
- ExAC SAS: 0.0667%
- gnomAD_E_EAS: 1.2411%
- gnomAD_E_FIN: 0.0314%
- gnomAD_E_NFE: 0.0314%
- gnomAD_E_OTH: 0.1835%
- gnomAD_E_SAS: 0.0661%
- gnomAD_G_EAS: 0.9259%
- gnomAD_G_NFE: 0.0267%
- gnomAD_G_OTH: 0.2037%
- Proximity score 0.500 in interactome to CPLANE2 and phenotypic similarity 0.744 to mouse mutant of CPLANE2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000562, polydactyly
- HP:0001363, Craniosynostosis - MP:0002639, micrognathia
- HP:0011304, Broad thumb - MP:0000562, polydactyly
- HP:0010055, Broad hallux - MP:0000562, polydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.731
Phenotype Score: 0.500
Variant Score: 0.989
- Pathogenicity Data:
- Best Score: 0.989303
- Polyphen2: 0.002 (B)
- Mutation Taster: 0.989 (P)
- SIFT: 0.318 (T)
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.530
Phenotype Score: 0.500
Variant Score: 0.894
- Pathogenicity Data:
- Best Score: 0.989303
- Polyphen2: 0.002 (B)
- Mutation Taster: 0.989 (P)
- SIFT: 0.318 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC EAS: 0.0116%
- gnomAD_E_EAS: 0.0174%
- Phenotypic similarity 0.286 to mouse mutant involving NEMP1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0002092, abnormal eye morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.500 in interactome to LEMD2 and phenotypic similarity 0.629 to Marbach-Rustad progeroid syndrome associated with LEMD2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0031846, Femur fracture
- HP:0001363, Craniosynostosis - HP:0002645, Wormian bones
- HP:0011304, Broad thumb - HP:0031846, Femur fracture
- HP:0010055, Broad hallux - HP:0031846, Femur fracture
- Proximity score 0.500 in interactome to LEMD2 and phenotypic similarity 0.257 to mouse mutant of LEMD2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0006069, abnormal retinal neuronal layer morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.731
Phenotype Score: 0.500
Variant Score: 0.989
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.999 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.021 (D)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0068%
- ExAC EAS: 0.0695%
- gnomAD_E_EAS: 0.0754%
- gnomAD_G_EAS: 0.0618%
- Proximity score 0.501 in interactome to ANXA1 and phenotypic similarity 0.631 to mouse mutant of ANXA1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0003843, abnormal sagittal suture morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.727
Phenotype Score: 0.501
Variant Score: 0.987
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0375%
- gnomAD_E_AMR: 0.0512%
- gnomAD_E_FIN: 0.0900%
- gnomAD_E_NFE: 0.0908%
- Proximity score 0.500 in interactome to CITED2 and phenotypic similarity 0.703 to Tetralogy of Fallot associated with CITED2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0000268, Dolichocephaly
- HP:0011304, Broad thumb - HP:0004209, Clinodactyly of the 5th finger
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Proximity score 0.500 in interactome to CITED2 and phenotypic similarity 0.320 to mouse mutant of CITED2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0000074, abnormal neurocranium morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.726
Phenotype Score: 0.500
Variant Score: 0.987
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.999 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.001 (D)
- Frequency Data:
- TOPMed: 0.0104%
- ExAC AFR: 0.0097%
- ExAC AMR: 0.0260%
- ExAC EAS: 0.0811%
- ExAC NFE: 0.0015%
- gnomAD_E_AFR: 0.0065%
- gnomAD_E_AMR: 0.0476%
- gnomAD_E_EAS: 0.0928%
- gnomAD_E_NFE: 0.0018%
- gnomAD_E_OTH: 0.0366%
- Proximity score 0.500 in interactome to HERC1 and phenotypic similarity 0.604 to Megalencephaly-severe kyphoscoliosis-overgrowth syndrome associated with HERC1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001166, Arachnodactyly
- HP:0001363, Craniosynostosis - HP:0011330, Metopic synostosis
- HP:0011304, Broad thumb - HP:0001166, Arachnodactyly
- HP:0010055, Broad hallux - HP:0001166, Arachnodactyly
- Proximity score 0.500 in interactome to HERC1 and phenotypic similarity 0.332 to mouse mutant of HERC1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.725
Phenotype Score: 0.500
Variant Score: 0.986
- Transcripts:
- CYTH4:ENST00000248901.6:c.1051G>A:p.(Glu351Lys)
- Pathogenicity Data:
- Best Score: 0.999999
- Polyphen2: 0.067 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.367 (T)
- Frequency Data:
- TOPMed: 0.0370%
- gnomAD_E_AMR: 0.0983%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_SAS: 0.0032%
- Proximity score 0.500 in interactome to ARVCF and phenotypic similarity 0.740 to 22q11.2 deletion syndrome associated with ARVCF.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001829, Foot polydactyly
- HP:0001363, Craniosynostosis - HP:0011324, Multiple suture craniosynostosis
- HP:0011304, Broad thumb - HP:0001161, Hand polydactyly
- HP:0010055, Broad hallux - HP:0001829, Foot polydactyly
- Proximity score 0.500 in interactome to ARVCF and phenotypic similarity 0.299 to mouse mutant of ARVCF.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001303, abnormal lens morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.721
Phenotype Score: 0.500
Variant Score: 0.984
- Pathogenicity Data:
- Best Score: 0.999929
- Polyphen2: 0.591 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.019 (D)
- Frequency Data:
- gnomAD_E_AFR: 0.0066%
- gnomAD_G_OTH: 0.1068%
- Pathogenicity Data:
- Best Score: 0.999961
- Polyphen2: 0.880 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.477 (T)
- Frequency Data:
- ExAC AFR: 0.0201%
- ExAC AMR: 0.0086%
- ExAC NFE: 0.0015%
- ExAC OTH: 0.1104%
- ExAC SAS: 0.0121%
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.910 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.051 (D)
- Frequency Data:
- gnomAD_E_AFR: 0.0173%
- gnomAD_E_AMR: 0.0596%
- gnomAD_E_EAS: 0.0615%
- gnomAD_E_FIN: 0.0624%
- gnomAD_E_NFE: 0.0925%
- gnomAD_E_OTH: 0.0225%
- gnomAD_E_SAS: 0.0267%
- gnomAD_G_AFR: 0.1270%
- gnomAD_G_AMR: 0.7782%
- gnomAD_G_EAS: 0.7075%
- gnomAD_G_FIN: 0.1679%
- gnomAD_G_NFE: 0.1013%
- gnomAD_G_OTH: 0.1420%
- Proximity score 0.500 in interactome to TOMM6 and phenotypic similarity 0.755 to mouse mutant of TOMM6.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
X_RECESSIVE
Exomiser Score: 0.716
Phenotype Score: 0.500
Variant Score: 0.981
- Pathogenicity Data:
- Best Score: 0.992
- Polyphen2: 0.992 (D)
- SIFT: 0.346 (T)
- Frequency Data:
- TOPMed: 0.0053%
- ExAC NFE: 0.0137%
- gnomAD_E_EAS: 0.0762%
- gnomAD_E_FIN: 0.0060%
- gnomAD_E_NFE: 0.0043%
X_DOMINANT
Exomiser Score: 0.716
Phenotype Score: 0.500
Variant Score: 0.981
- Pathogenicity Data:
- Best Score: 0.992
- Polyphen2: 0.992 (D)
- SIFT: 0.346 (T)
- Frequency Data:
- TOPMed: 0.0053%
- ExAC NFE: 0.0137%
- gnomAD_E_EAS: 0.0762%
- gnomAD_E_FIN: 0.0060%
- gnomAD_E_NFE: 0.0043%
- Phenotypic similarity 0.487 to Multiple pterygium syndrome, lethal type associated with CHRND.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0009381, Short finger
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009381, Short finger
- HP:0010055, Broad hallux - HP:0009381, Short finger
- Phenotypic similarity 0.272 to mouse mutant involving CHRND.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001297, microphthalmia
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.500 in interactome to LAMA5 and phenotypic similarity 0.739 to mouse mutant of LAMA5.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
- Known diseases:
- OMIM:253290 Multiple pterygium syndrome, lethal type - autosomal recessive
- OMIM:616321 ?Myasthenic syndrome, congenital, 3A, slow-channel (unconfirmed)
- OMIM:616322 Myasthenic syndrome, congenital, 3B, fast-channel - autosomal recessive
- OMIM:616323 ?Myasthenic syndrome, congenital, 3C, associated with acetylcholine receptor deficiency (unconfirmed)
- ORPHA:98913 Postsynaptic congenital myasthenic syndromes - autosomal dominant
- ORPHA:98913 Postsynaptic congenital myasthenic syndromes - autosomal recessive
- ORPHA:98913 Postsynaptic congenital myasthenic syndromes - autosomal recessive
- ORPHA:98913 Postsynaptic congenital myasthenic syndromes - autosomal dominant
- ORPHA:98913 Postsynaptic congenital myasthenic syndromes - autosomal recessive
- ORPHA:98913 Postsynaptic congenital myasthenic syndromes - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.715
Phenotype Score: 0.500
Variant Score: 0.981
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.170 to ORPHA:98913 Postsynaptic congenital myasthenic syndromes
- Pathogenicity Data:
- Best Score: 0.981024
- Polyphen2: 0.380 (B)
- Mutation Taster: 0.981 (P)
- SIFT: 0.044 (D)
- Frequency Data:
- No frequency data
- Proximity score 0.503 in interactome to CTCF and phenotypic similarity 0.750 to CTCF-related neurodevelopmental disorder associated with CTCF.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0004691, 2-3 toe syndactyly
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0010059, Broad hallux phalanx
- HP:0010055, Broad hallux - HP:0010059, Broad hallux phalanx
- Proximity score 0.503 in interactome to CTCF and phenotypic similarity 0.335 to fish mutant of CTCF.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - ZP:0002314, head shape, abnormal
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.714
Phenotype Score: 0.503
Variant Score: 0.977
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.002 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.174 (T)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0088%
- ESP AA: 0.0228%
- ESP All: 0.0077%
- ExAC AFR: 0.0112%
- ExAC EAS: 0.0846%
- ExAC NFE: 0.0017%
- gnomAD_E_EAS: 0.1085%
- gnomAD_E_NFE: 0.0011%
- gnomAD_G_AFR: 0.0115%
- Pathogenicity Data:
- Best Score: 0.986
- Polyphen2: 0.001 (B)
- SIFT: 0.014 (D)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0080%
- ExAC EAS: 0.0835%
- gnomAD_E_EAS: 0.1169%
- gnomAD_G_AFR: 0.0115%
- Pathogenicity Data:
- Best Score: 0.952
- Polyphen2: 0.357 (B)
- SIFT: 0.048 (D)
- Frequency Data:
- 1000Genomes: 0.2196%
- TOPMed: 0.0265%
- ExAC EAS: 0.7884%
- ExAC OTH: 0.1289%
- ExAC SAS: 0.0132%
- gnomAD_E_EAS: 0.7221%
- gnomAD_E_OTH: 0.0376%
- gnomAD_E_SAS: 0.0066%
- gnomAD_G_EAS: 0.4932%
- Proximity score 0.500 in interactome to CPLX1 and phenotypic similarity 0.628 to Wolf-Hirschhorn syndrome associated with CPLX1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0009778, Short thumb
- HP:0001363, Craniosynostosis - HP:0001362, Calvarial skull defect
- HP:0011304, Broad thumb - HP:0001177, Preaxial hand polydactyly
- HP:0010055, Broad hallux - HP:0010109, Short hallux
X_RECESSIVE
Exomiser Score: 0.713
Phenotype Score: 0.500
Variant Score: 0.980
- Pathogenicity Data:
- Best Score: 0.993676
- Polyphen2: 0.003 (B)
- Mutation Taster: 0.994 (P)
- SIFT: 0.018 (D)
- Frequency Data:
- TOPMed: 0.0019%
- ExAC EAS: 0.0302%
- gnomAD_E_EAS: 0.0467%
- gnomAD_G_EAS: 0.0986%
X_DOMINANT
Exomiser Score: 0.713
Phenotype Score: 0.500
Variant Score: 0.980
- Pathogenicity Data:
- Best Score: 0.993676
- Polyphen2: 0.003 (B)
- Mutation Taster: 0.994 (P)
- SIFT: 0.018 (D)
- Frequency Data:
- TOPMed: 0.0019%
- ExAC EAS: 0.0302%
- gnomAD_E_EAS: 0.0467%
- gnomAD_G_EAS: 0.0986%
- Phenotypic similarity 0.769 to mouse mutant involving FBXW12.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis - MP:0005270, abnormal zygomatic bone morphology
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.706
Phenotype Score: 0.769
Variant Score: 0.672
- Pathogenicity Data:
- Best Score: 0.678
- Polyphen2: 0.030 (B)
- SIFT: 0.322 (T)
- Frequency Data:
- TOPMed: 0.0019%
- gnomAD_G_EAS: 0.0617%
- Phenotypic similarity 0.487 to mouse mutant involving HHIPL1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0004357, long tibia
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0004357, long tibia
- HP:0010055, Broad hallux - MP:0004357, long tibia
AUTOSOMAL_DOMINANT
Exomiser Score: 0.706
Phenotype Score: 0.487
Variant Score: 0.991
- Pathogenicity Data:
- Best Score: 0.999671
- Polyphen2: 0.997 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.004 (D)
- Frequency Data:
- TOPMed: 0.0008%
- gnomAD_G_EAS: 0.0618%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.033
Phenotype Score: 0.487
Variant Score: 0.529
- Pathogenicity Data:
- Best Score: 0.999671
- Polyphen2: 0.997 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.004 (D)
- Frequency Data:
- TOPMed: 0.0008%
- gnomAD_G_EAS: 0.0618%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.2196%
- TOPMed: 0.0412%
- ExAC EAS: 0.9718%
- ExAC OTH: 0.1111%
- ExAC SAS: 0.0061%
- gnomAD_E_EAS: 0.8699%
- gnomAD_E_NFE: 0.0018%
- gnomAD_E_OTH: 0.0182%
- gnomAD_E_SAS: 0.0032%
- gnomAD_G_EAS: 1.2346%
- Phenotypic similarity 0.320 to mouse mutant involving AKAP13.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0002092, abnormal eye morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.503 in interactome to ARHGAP31 and phenotypic similarity 0.698 to Adams-Oliver syndrome 1 associated with ARHGAP31.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0001362, Calvarial skull defect
- HP:0011304, Broad thumb - HP:0001156, Brachydactyly
- HP:0010055, Broad hallux - HP:0001770, Toe syndactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.699
Phenotype Score: 0.503
Variant Score: 0.969
- Pathogenicity Data:
- Best Score: 0.972
- Polyphen2: 0.897 (P)
- SIFT: 0.028 (D)
- Frequency Data:
- TOPMed: 0.0045%
- ESP AA: 0.0227%
- ESP All: 0.0077%
- ExAC AFR: 0.0096%
- gnomAD_E_AFR: 0.0065%
- gnomAD_G_AFR: 0.0115%
- Proximity score 0.500 in interactome to SCLT1 and phenotypic similarity 0.720 to mouse mutant of SCLT1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0009743, preaxial polydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0009743, preaxial polydactyly
- HP:0010055, Broad hallux - MP:0009743, preaxial polydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.684
Phenotype Score: 0.500
Variant Score: 0.965
- Transcripts:
- OR6A2:ENST00000332601.3:c.715C>T:p.(Arg239Cys)
- Pathogenicity Data:
- Best Score: 0.967
- Polyphen2: 0.051 (B)
- SIFT: 0.033 (D)
- Frequency Data:
- TOPMed: 0.0042%
- UK10K: 0.0132%
- ExAC AFR: 0.0096%
- ExAC AMR: 0.0087%
- ExAC NFE: 0.0015%
- ExAC SAS: 0.0061%
- gnomAD_E_AFR: 0.0131%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_FIN: 0.0090%
- gnomAD_E_NFE: 0.0018%
- gnomAD_E_SAS: 0.0065%
- gnomAD_G_AFR: 0.0115%
- gnomAD_G_NFE: 0.0133%
- Proximity score 0.500 in interactome to MYOZ1 and phenotypic similarity 0.737 to mouse mutant of MYOZ1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000565, oligodactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0000565, oligodactyly
- HP:0010055, Broad hallux - MP:0000565, oligodactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.676
Phenotype Score: 0.500
Variant Score: 0.961
- Pathogenicity Data:
- Best Score: 0.961
- Polyphen2: 0.004 (B)
- SIFT: 0.039 (D)
- Frequency Data:
- No frequency data
- Proximity score 0.500 in interactome to MOGS and phenotypic similarity 0.479 to Congenital disorder of glycosylation, type IIb associated with MOGS.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010557, Overlapping fingers
- HP:0001363, Craniosynostosis - HP:0000269, Prominent occiput
- HP:0011304, Broad thumb - HP:0010557, Overlapping fingers
- HP:0010055, Broad hallux - HP:0010557, Overlapping fingers
- Proximity score 0.500 in interactome to MOGS and phenotypic similarity 0.920 to mouse mutant of MOGS.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002544, brachydactyly
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb - MP:0002544, brachydactyly
- HP:0010055, Broad hallux - MP:0002544, brachydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.665
Phenotype Score: 0.500
Variant Score: 0.955
- Pathogenicity Data:
- Best Score: 0.957
- Polyphen2: 0.082 (B)
- SIFT: 0.043 (D)
- Frequency Data:
- TOPMed: 0.0004%
- ExAC EAS: 0.0128%
- gnomAD_E_EAS: 0.0058%
- Proximity score 0.500 in interactome to ACTG1 and phenotypic similarity 0.706 to Baraitser-Winter cerebrofrontofacial syndrome associated with ACTG1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0009942, Duplication of thumb phalanx
- HP:0001363, Craniosynostosis - HP:0005487, Prominent metopic ridge
- HP:0011304, Broad thumb - HP:0009942, Duplication of thumb phalanx
- HP:0010055, Broad hallux - HP:0009942, Duplication of thumb phalanx
- Proximity score 0.500 in interactome to ACTG1 and phenotypic similarity 0.215 to mouse mutant of ACTG1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0004521, abnormal cochlear hair cell stereociliary bundle morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.661
Phenotype Score: 0.500
Variant Score: 0.954
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.011 (D)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0091%
- ExAC AMR: 0.0879%
- gnomAD_E_AMR: 0.1443%
- gnomAD_E_OTH: 0.0580%
- gnomAD_G_AMR: 0.1193%
- Pathogenicity Data:
- Best Score: 0.982
- SIFT: 0.018 (D)
- Frequency Data:
- 1000Genomes: 0.0599%
- TOPMed: 0.0518%
- ESP AA: 0.0723%
- ESP All: 0.0219%
- ExAC AFR: 0.1105%
- gnomAD_E_AFR: 0.0684%
- gnomAD_E_AMR: 0.0126%
- gnomAD_E_EAS: 0.3389%
- gnomAD_E_NFE: 0.0036%
- gnomAD_E_OTH: 0.0269%
- gnomAD_E_SAS: 0.0044%
- gnomAD_G_AFR: 0.0923%
- gnomAD_G_EAS: 0.1235%
- Proximity score 0.500 in interactome to SIK3 and phenotypic similarity 0.670 to ?Spondyloepimetaphyseal dysplasia, Krakow type associated with SIK3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0002691, Platybasia
- HP:0011304, Broad thumb - HP:0001156, Brachydactyly
- HP:0010055, Broad hallux - HP:0004691, 2-3 toe syndactyly
- Proximity score 0.500 in interactome to SIK3 and phenotypic similarity 0.812 to mouse mutant of SIK3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0011504, abnormal limb long bone morphology
- HP:0001363, Craniosynostosis - MP:0010743, delayed cranial suture closure
- HP:0011304, Broad thumb - MP:0011504, abnormal limb long bone morphology
- HP:0010055, Broad hallux - MP:0004509, abnormal pelvic girdle bone morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.649
Phenotype Score: 0.500
Variant Score: 0.948
- Pathogenicity Data:
- Best Score: 0.956
- Polyphen2: 0.684 (P)
- SIFT: 0.044 (D)
- Frequency Data:
- TOPMed: 0.0072%
- ExAC EAS: 0.0232%
- ExAC NFE: 0.0030%
- ExAC SAS: 0.0121%
- gnomAD_E_EAS: 0.0406%
- gnomAD_E_NFE: 0.0036%
- gnomAD_E_OTH: 0.0182%
- gnomAD_E_SAS: 0.0195%
- gnomAD_G_EAS: 0.0617%
- gnomAD_G_NFE: 0.0400%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.595
Phenotype Score: 0.500
Variant Score: 0.923
- Pathogenicity Data:
- Best Score: 0.956
- Polyphen2: 0.684 (P)
- SIFT: 0.044 (D)
- Frequency Data:
- TOPMed: 0.0072%
- ExAC EAS: 0.0232%
- ExAC NFE: 0.0030%
- ExAC SAS: 0.0121%
- gnomAD_E_EAS: 0.0406%
- gnomAD_E_NFE: 0.0036%
- gnomAD_E_OTH: 0.0182%
- gnomAD_E_SAS: 0.0195%
- gnomAD_G_EAS: 0.0617%
- gnomAD_G_NFE: 0.0400%
- Transcripts:
- ACSM5:ENST00000331849.4:c.901G>C:p.(Asp301His)
- Pathogenicity Data:
- Best Score: 0.998
- Polyphen2: 0.972 (D)
- Mutation Taster: 0.960 (P)
- SIFT: 0.002 (D)
- Frequency Data:
- 1000Genomes: 0.0599%
- TOPMed: 0.0350%
- ExAC EAS: 0.3934%
- gnomAD_E_EAS: 0.4177%
- gnomAD_G_EAS: 0.5556%
- Phenotypic similarity 0.449 to ?Immunodeficiency 59 and hypoglycemia associated with HYOU1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001238, Slender finger
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001238, Slender finger
- HP:0010055, Broad hallux - HP:0001238, Slender finger
- Proximity score 0.527 in interactome to SIL1 and phenotypic similarity 0.631 to Marinesco-Sjögren syndrome associated with SIL1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0010508, Metatarsus valgus
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Known diseases:
- OMIM:233600 ?Immunodeficiency 59 and hypoglycemia (unconfirmed)
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.647
Phenotype Score: 0.527
Variant Score: 0.917
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.449 to OMIM:233600 ?Immunodeficiency 59 and hypoglycemia
- Pathogenicity Data:
- Best Score: 0.99958
- Polyphen2: 0.975 (D)
- Mutation Taster: 1.000 (P)
- Frequency Data:
- 1000Genomes: 0.0599%
- TOPMed: 0.0083%
- ExAC AMR: 0.0519%
- ExAC EAS: 0.0928%
- ExAC FIN: 0.0454%
- ExAC NFE: 0.0045%
- gnomAD_E_AFR: 0.0065%
- gnomAD_E_AMR: 0.0238%
- gnomAD_E_EAS: 0.0986%
- gnomAD_E_FIN: 0.0202%
- gnomAD_E_NFE: 0.0027%
- gnomAD_G_EAS: 0.1233%
- gnomAD_G_FIN: 0.0286%
- gnomAD_G_NFE: 0.0067%
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.998 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.189 (T)
- Frequency Data:
- 1000Genomes: 0.0799%
- TOPMed: 0.0193%
- ExAC EAS: 0.4397%
- ExAC SAS: 0.0372%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_EAS: 0.4290%
- gnomAD_E_SAS: 0.0325%
- gnomAD_G_EAS: 0.7417%
- Proximity score 0.500 in interactome to CPLX1 and phenotypic similarity 0.628 to Wolf-Hirschhorn syndrome associated with CPLX1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0009778, Short thumb
- HP:0001363, Craniosynostosis - HP:0001362, Calvarial skull defect
- HP:0011304, Broad thumb - HP:0001177, Preaxial hand polydactyly
- HP:0010055, Broad hallux - HP:0010109, Short hallux
AUTOSOMAL_DOMINANT
Exomiser Score: 0.644
Phenotype Score: 0.500
Variant Score: 0.945
- Pathogenicity Data:
- Best Score: 0.958
- Polyphen2: 0.002 (B)
- SIFT: 0.042 (D)
- Frequency Data:
- TOPMed: 0.0064%
- ExAC EAS: 0.0833%
- gnomAD_E_EAS: 0.0937%
- gnomAD_E_SAS: 0.0033%
- Phenotypic similarity 0.265 to mouse mutant involving PER1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0005605, increased bone mass
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.508 in interactome to NONO and phenotypic similarity 0.699 to Intellectual developmental disorder, X-linked syndromic 34 associated with NONO.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001822, Hallux valgus
- HP:0001363, Craniosynostosis - HP:0002684, Thickened calvaria
- HP:0011304, Broad thumb - HP:0001822, Hallux valgus
- HP:0010055, Broad hallux - HP:0001822, Hallux valgus
AUTOSOMAL_DOMINANT
Exomiser Score: 0.631
Phenotype Score: 0.508
Variant Score: 0.930
- Pathogenicity Data:
- Best Score: 0.93
- Polyphen2: 0.007 (B)
- SIFT: 0.070 (T)
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.670 to Blackfan-Diamond anemia associated with GATA1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0009778, Short thumb
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001199, Triphalangeal thumb
- HP:0010055, Broad hallux - HP:0001199, Triphalangeal thumb
- Phenotypic similarity 0.344 to mouse mutant involving GATA1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0020039, increased bone ossification
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.510 in interactome to ZFPM2 and phenotypic similarity 0.703 to Tetralogy of Fallot associated with ZFPM2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0000268, Dolichocephaly
- HP:0011304, Broad thumb - HP:0004209, Clinodactyly of the 5th finger
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Known diseases:
- OMIM:190685 Leukemia, megakaryoblastic, with or without Down syndrome, somatic - unknown
- OMIM:300367 Thrombocytopenia, X-linked, with or without dyserythropoietic anemia - X-linked recessive
- OMIM:300835 Anemia, X-linked, with/without neutropenia and/or platelet abnormalities - X-linked recessive
- OMIM:314050 Thrombocytopenia with beta-thalassemia, X-linked - X-linked recessive
- ORPHA:124 Blackfan-Diamond anemia - autosomal dominant
- ORPHA:231393 Beta-thalassemia-X-linked thrombocytopenia syndrome - X-linked recessive
- ORPHA:67044 Thrombocytopenia with congenital dyserythropoietic anemia - X-linked recessive
- ORPHA:79277 Congenital erythropoietic porphyria - autosomal recessive
X_RECESSIVE
Exomiser Score: 0.623
Phenotype Score: 0.510
Variant Score: 0.925
- Pathogenicity Data:
- Best Score: 0.935
- Polyphen2: 0.026 (B)
- SIFT: 0.065 (T)
- Frequency Data:
- 1000Genomes: 0.0265%
- TOPMed: 0.0120%
- ExAC EAS: 0.0754%
- gnomAD_E_EAS: 0.0777%
X_DOMINANT
Exomiser Score: 0.105
Phenotype Score: 0.255
Variant Score: 0.925
- Pathogenicity Data:
- Best Score: 0.935
- Polyphen2: 0.026 (B)
- SIFT: 0.065 (T)
- Frequency Data:
- 1000Genomes: 0.0265%
- TOPMed: 0.0120%
- ExAC EAS: 0.0754%
- gnomAD_E_EAS: 0.0777%
- Proximity score 0.500 in interactome to UBE4B and phenotypic similarity 0.667 to 1p36 deletion syndrome associated with UBE4B.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0000270, Delayed cranial suture closure
- HP:0011304, Broad thumb - HP:0100490, Camptodactyly of finger
- HP:0010055, Broad hallux - HP:0001829, Foot polydactyly
- Known diseases:
- OMIM:164400 Spinocerebellar ataxia 1 - autosomal dominant
- ORPHA:98755 Spinocerebellar ataxia type 1 - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.622
Phenotype Score: 0.500
Variant Score: 0.935
- Pathogenicity Data:
- Best Score: 0.935
- Polyphen2: 0.227 (B)
- SIFT: 0.065 (T)
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.076
Phenotype Score: 0.250
Variant Score: 0.893
- Pathogenicity Data:
- Best Score: 0.935
- Polyphen2: 0.227 (B)
- SIFT: 0.065 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.502 in interactome to RBPJ and phenotypic similarity 0.662 to Adams-Oliver syndrome associated with RBPJ.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0001362, Calvarial skull defect
- HP:0011304, Broad thumb - HP:0009882, Short distal phalanx of finger
- HP:0010055, Broad hallux - HP:0010760, Absent toe
- Proximity score 0.502 in interactome to RBPJ and phenotypic similarity 0.245 to mouse mutant of RBPJ.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0010124, decreased bone mineral content
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.615
Phenotype Score: 0.502
Variant Score: 0.929
- Transcripts:
- MAML3:ENST00000509479.2:c.3142A>G:p.(Met1048Val)
- Pathogenicity Data:
- Best Score: 0.992
- Mutation Taster: 0.968 (P)
- SIFT: 0.008 (D)
- Frequency Data:
- 1000Genomes: 0.0799%
- TOPMed: 0.0129%
- ExAC EAS: 0.2514%
- ExAC NFE: 0.0031%
- ExAC SAS: 0.0441%
- gnomAD_E_EAS: 0.2507%
- gnomAD_E_NFE: 0.0027%
- gnomAD_E_SAS: 0.0294%
- gnomAD_G_EAS: 0.3090%
- Pathogenicity Data:
- Best Score: 0.932
- Polyphen2: 0.022 (B)
- SIFT: 0.068 (T)
- Frequency Data:
- 1000Genomes: 0.0599%
- TOPMed: 0.0026%
- ExAC AFR: 0.0116%
- ExAC EAS: 0.0302%
- gnomAD_E_AFR: 0.0067%
- gnomAD_E_EAS: 0.0237%
- gnomAD_E_SAS: 0.0033%
- gnomAD_G_EAS: 0.1233%
- Proximity score 0.506 in interactome to SIAH1 and phenotypic similarity 0.858 to Buratti-Harel syndrome associated with SIAH1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010055, Broad hallux
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0011304, Broad thumb
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
AUTOSOMAL_DOMINANT
Exomiser Score: 0.614
Phenotype Score: 0.506
Variant Score: 0.925
- Transcripts:
- PEG3:ENST00000326441.9:c.2072G>A:p.(Arg691Gln)
- PEG3:ENST00000423103.2:c.2072G>A:p.(Arg691Gln)
- PEG3:ENST00000593695.1:c.1694G>A:p.(Arg565Gln)
- PEG3:ENST00000598410.1:c.1700G>A:p.(Arg567Gln)
- PEG3:ENST00000221722.5:c.397+2230G>A:p.(=)
- PEG3:ENST00000391708.3:c.397+2230G>A:p.(=)
- PEG3:ENST00000593711.1:c.397+2230G>A:p.(=)
- PEG3:ENST00000599935.1:c.397+2230G>A:p.(=)
- PEG3:ENST00000601070.1:c.397+2230G>A:p.(=)
- Pathogenicity Data:
- Best Score: 0.93
- Polyphen2: 0.428 (B)
- SIFT: 0.070 (T)
- Frequency Data:
- 1000Genomes: 0.0399%
- TOPMed: 0.0087%
- ESP EA: 0.0116%
- ESP All: 0.0077%
- ExAC AFR: 0.0098%
- ExAC EAS: 0.0116%
- ExAC NFE: 0.0060%
- gnomAD_E_AFR: 0.0065%
- gnomAD_E_AMR: 0.0060%
- gnomAD_E_EAS: 0.0116%
- gnomAD_E_NFE: 0.0108%
- gnomAD_G_NFE: 0.0133%
- Proximity score 0.501 in interactome to PTPN11 and phenotypic similarity 0.656 to Noonan syndrome 1 associated with PTPN11.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009466, Radial deviation of finger
- HP:0010055, Broad hallux - HP:0030084, Clinodactyly
- Proximity score 0.501 in interactome to PTPN11 and phenotypic similarity 0.540 to mouse mutant of PTPN11.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0012514, pectus excavatum
- HP:0001363, Craniosynostosis - MP:0010031, abnormal cranium size
- HP:0011304, Broad thumb - MP:0012514, pectus excavatum
- HP:0010055, Broad hallux - MP:0012514, pectus excavatum
AUTOSOMAL_DOMINANT
Exomiser Score: 0.612
Phenotype Score: 0.501
Variant Score: 0.930
- Pathogenicity Data:
- Best Score: 0.93
- Polyphen2: 0.001 (B)
- SIFT: 0.070 (T)
- Frequency Data:
- No frequency data
- Proximity score 0.500 in interactome to RFWD3 and phenotypic similarity 0.676 to Fanconi anemia associated with RFWD3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001770, Toe syndactyly
- HP:0001363, Craniosynostosis - HP:0000268, Dolichocephaly
- HP:0011304, Broad thumb - HP:0001199, Triphalangeal thumb
- HP:0010055, Broad hallux - HP:0001770, Toe syndactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.606
Phenotype Score: 0.500
Variant Score: 0.928
- Pathogenicity Data:
- Best Score: 0.928
- Polyphen2: 0.343 (B)
- SIFT: 0.072 (T)
- Frequency Data:
- No frequency data
- Proximity score 0.500 in interactome to RSPO2 and phenotypic similarity 0.468 to ?Humerofemoral hypoplasia with radiotibial ray deficiency associated with RSPO2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0003865, Bowed humerus
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009777, Absent thumb
- HP:0010055, Broad hallux - HP:0009777, Absent thumb
- Proximity score 0.500 in interactome to RSPO2 and phenotypic similarity 0.727 to mouse mutant of RSPO2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0005306, abnormal phalanx morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
- Proximity score 0.500 in interactome to RSPO2 and phenotypic similarity 0.233 to fish mutant of RSPO2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - ZP:0012192, rib hypoplastic, abnormal
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.597
Phenotype Score: 0.500
Variant Score: 0.924
- Transcripts:
- OTOL1:ENST00000327928.4:c.1207A>C:p.(Ile403Leu)
- Pathogenicity Data:
- Best Score: 0.924
- Polyphen2: 0.621 (P)
- SIFT: 0.076 (T)
- Frequency Data:
- No frequency data
- Proximity score 0.500 in interactome to B3GLCT and phenotypic similarity 0.709 to Peters-plus syndrome associated with B3GLCT.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0009623, Proximal placement of thumb
- HP:0010055, Broad hallux - HP:0001831, Short toe
- Proximity score 0.500 in interactome to B3GLCT and phenotypic similarity 0.841 to mouse mutant of B3GLCT.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002544, brachydactyly
- HP:0001363, Craniosynostosis - MP:0008273, abnormal intramembranous bone ossification
- HP:0011304, Broad thumb - MP:0002544, brachydactyly
- HP:0010055, Broad hallux - MP:0002544, brachydactyly
- Known diseases:
- OMIM:219050 Cryptorchidism - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.589
Phenotype Score: 0.500
Variant Score: 0.920
- Pathogenicity Data:
- Best Score: 0.923
- Polyphen2: 0.002 (B)
- SIFT: 0.077 (T)
- Frequency Data:
- TOPMed: 0.0072%
- gnomAD_E_AFR: 0.0158%
- gnomAD_E_EAS: 0.0100%
- gnomAD_E_SAS: 0.0044%
- gnomAD_G_AFR: 0.0229%
- gnomAD_G_NFE: 0.0067%
- Phenotypic similarity 0.486 to mouse mutant involving GLG1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0006396, decreased long bone epiphyseal plate size
- HP:0001363, Craniosynostosis - MP:0003795, abnormal bone structure
- HP:0011304, Broad thumb - MP:0006396, decreased long bone epiphyseal plate size
- HP:0010055, Broad hallux - MP:0006396, decreased long bone epiphyseal plate size
- Proximity score 0.500 in interactome to PIBF1 and phenotypic similarity 0.613 to Joubert syndrome associated with PIBF1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001829, Foot polydactyly
- HP:0001363, Craniosynostosis - HP:0004422, Biparietal narrowing
- HP:0011304, Broad thumb - HP:0001161, Hand polydactyly
- HP:0010055, Broad hallux - HP:0001829, Foot polydactyly
- Proximity score 0.500 in interactome to PIBF1 and phenotypic similarity 0.278 to mouse mutant of PIBF1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001303, abnormal lens morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.569
Phenotype Score: 0.500
Variant Score: 0.911
- Pathogenicity Data:
- Best Score: 0.911
- Polyphen2: 0.009 (B)
- SIFT: 0.089 (T)
- Frequency Data:
- No frequency data
- Proximity score 0.500 in interactome to SCLT1 and phenotypic similarity 0.720 to mouse mutant of SCLT1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0009743, preaxial polydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0009743, preaxial polydactyly
- HP:0010055, Broad hallux - MP:0009743, preaxial polydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.566
Phenotype Score: 0.500
Variant Score: 0.910
- Transcripts:
- OR4K13:ENST00000315693.2:c.769A>G:p.(Ile257Val)
- Pathogenicity Data:
- Best Score: 0.916
- Polyphen2: 0.458 (P)
- SIFT: 0.084 (T)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0104%
- ESP EA: 0.0116%
- ESP All: 0.0077%
- ExAC EAS: 0.0463%
- ExAC NFE: 0.0120%
- ExAC SAS: 0.0182%
- gnomAD_E_EAS: 0.0348%
- gnomAD_E_NFE: 0.0072%
- gnomAD_E_OTH: 0.0183%
- gnomAD_E_SAS: 0.0163%
- gnomAD_G_NFE: 0.0200%
- Phenotypic similarity 0.397 to mouse mutant involving REXO1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0005650, abnormal limb bud morphology
- HP:0001363, Craniosynostosis - MP:0001293, anophthalmia
- HP:0011304, Broad thumb - MP:0005650, abnormal limb bud morphology
- HP:0010055, Broad hallux - MP:0005650, abnormal limb bud morphology
- Proximity score 0.500 in interactome to RAI1 and phenotypic similarity 0.701 to Smith-Magenis syndrome associated with RAI1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0000248, Brachycephaly
- HP:0011304, Broad thumb - HP:0001161, Hand polydactyly
- HP:0010055, Broad hallux - HP:0001770, Toe syndactyly
- Proximity score 0.500 in interactome to RAI1 and phenotypic similarity 0.699 to mouse mutant of RAI1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000413, polyphalangy
- HP:0001363, Craniosynostosis - MP:0002260, abnormal thyroid cartilage morphology
- HP:0011304, Broad thumb - MP:0000413, polyphalangy
- HP:0010055, Broad hallux - MP:0000413, polyphalangy
AUTOSOMAL_DOMINANT
Exomiser Score: 0.545
Phenotype Score: 0.500
Variant Score: 0.900
- Transcripts:
- REXO1:ENST00000170168.4:c.1919A>G:p.(Lys640Arg)
- Pathogenicity Data:
- Best Score: 0.908
- Polyphen2: 0.031 (B)
- Mutation Taster: 0.592
- SIFT: 0.092 (T)
- Frequency Data:
- TOPMed: 0.0019%
- ExAC EAS: 0.0463%
- ExAC NFE: 0.0015%
- gnomAD_E_EAS: 0.0406%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_SAS: 0.0065%
- gnomAD_G_EAS: 0.0617%
- Proximity score 0.500 in interactome to HSPG2 and phenotypic similarity 0.667 to 1p36 deletion syndrome associated with HSPG2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0000270, Delayed cranial suture closure
- HP:0011304, Broad thumb - HP:0100490, Camptodactyly of finger
- HP:0010055, Broad hallux - HP:0001829, Foot polydactyly
- Proximity score 0.500 in interactome to HSPG2 and phenotypic similarity 0.701 to mouse mutant of HSPG2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0006397, disorganized long bone epiphyseal plate
- HP:0001363, Craniosynostosis - MP:0030029, wide cranial sutures
- HP:0011304, Broad thumb - MP:0006397, disorganized long bone epiphyseal plate
- HP:0010055, Broad hallux - MP:0006397, disorganized long bone epiphyseal plate
AUTOSOMAL_DOMINANT
Exomiser Score: 0.535
Phenotype Score: 0.500
Variant Score: 0.896
- Pathogenicity Data:
- Best Score: 0.899
- Polyphen2: 0.770 (P)
- SIFT: 0.101 (T)
- Frequency Data:
- TOPMed: 0.0004%
- ExAC EAS: 0.0231%
- gnomAD_E_EAS: 0.0116%
- Phenotypic similarity 0.537 to X-linked intellectual disability, Siderius type associated with PHF8.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001177, Preaxial hand polydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001177, Preaxial hand polydactyly
- HP:0010055, Broad hallux - HP:0001177, Preaxial hand polydactyly
- Phenotypic similarity 0.307 to mouse mutant involving PHF8.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0000062, increased bone mineral density
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Known diseases:
- OMIM:300263 Intellectual developmental disorder, X-linked, syndromic, Siderius type - X-linked recessive
- ORPHA:85287 X-linked intellectual disability, Siderius type - X-linked recessive
X_RECESSIVE
Exomiser Score: 0.521
Phenotype Score: 0.537
Variant Score: 0.849
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.537 to ORPHA:85287 X-linked intellectual disability, Siderius type
- Phenotypic similarity 0.530 to OMIM:300263 Intellectual developmental disorder, X-linked, syndromic, Siderius type
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AMR: 0.0039%
- gnomAD_E_FIN: 0.0064%
- gnomAD_E_NFE: 0.0090%
X_DOMINANT
Exomiser Score: 0.020
Phenotype Score: 0.153
Variant Score: 0.849
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AMR: 0.0039%
- gnomAD_E_FIN: 0.0064%
- gnomAD_E_NFE: 0.0090%
- Phenotypic similarity 0.295 to Kallmann syndrome associated with ANOS1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux - HP:0001761, Pes cavus
- Proximity score 0.500 in interactome to IDUA and phenotypic similarity 0.477 to Hurler syndrome associated with IDUA.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0100490, Camptodactyly of finger
- HP:0001363, Craniosynostosis - HP:0000268, Dolichocephaly
- HP:0011304, Broad thumb - HP:0100490, Camptodactyly of finger
- HP:0010055, Broad hallux - HP:0100490, Camptodactyly of finger
- Proximity score 0.500 in interactome to IDUA and phenotypic similarity 0.724 to mouse mutant of IDUA.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis - MP:0000441, increased cranium width
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
- Known diseases:
- OMIM:308700 Hypogonadotropic hypogonadism 1 with or without anosmia (Kallmann syndrome 1) - X-linked recessive
- ORPHA:478 Kallmann syndrome - X-linked recessive
X_RECESSIVE
Exomiser Score: 0.521
Phenotype Score: 0.500
Variant Score: 0.890
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.295 to ORPHA:478 Kallmann syndrome
- Phenotypic similarity 0.274 to OMIM:308700 Hypogonadotropic hypogonadism 1 with or without anosmia (Kallmann syndrome 1)
- Transcripts:
- ANOS1:ENST00000262648.3:c.1511C>T:p.(Pro504Leu)
- Pathogenicity Data:
- Best Score: 0.93299997
- Polyphen2: 0.005 (B)
- SIFT: 0.067 (T)
- Frequency Data:
- 1000Genomes: 0.0530%
- TOPMed: 0.0140%
- ExAC AMR: 0.0114%
- ExAC EAS: 0.2718%
- ExAC NFE: 0.0023%
- ExAC SAS: 0.0459%
- gnomAD_E_AMR: 0.0188%
- gnomAD_E_EAS: 0.2339%
- gnomAD_E_NFE: 0.0025%
- gnomAD_E_SAS: 0.0476%
- gnomAD_G_EAS: 0.2935%
- Proximity score 0.500 in interactome to TONSL and phenotypic similarity 0.610 to SPONASTRIME dysplasia associated with TONSL.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0002007, Frontal bossing
- HP:0011304, Broad thumb - HP:0010234, Ivory epiphyses of the phalanges of the hand
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Proximity score 0.500 in interactome to TONSL and phenotypic similarity 0.244 to mouse mutant of TONSL.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0002792, abnormal retinal vasculature morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.500 in interactome to TONSL and phenotypic similarity 0.415 to fish mutant of TONSL.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - ZP:0010247, ossification increased occurrence, abnormal
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.513
Phenotype Score: 0.500
Variant Score: 0.887
- Pathogenicity Data:
- Best Score: 0.886801
- Polyphen2: 0.001 (B)
- Mutation Taster: 0.887
- Frequency Data:
- TOPMed: 0.0004%
- Phenotypic similarity 0.434 to Autosomal recessive centronuclear myopathy associated with TTN.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0100807, Long fingers
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0100807, Long fingers
- HP:0010055, Broad hallux - HP:0100807, Long fingers
- Phenotypic similarity 0.332 to mouse mutant involving TTN.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0010225, abnormal quadriceps morphology
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0010225, abnormal quadriceps morphology
- HP:0010055, Broad hallux - MP:0010225, abnormal quadriceps morphology
- Known diseases:
- OMIM:600334 Tibial muscular dystrophy, tardive - autosomal dominant
- OMIM:603689 Myopathy, myofibrillar, 9, with early respiratory failure - autosomal dominant
- OMIM:604145 Cardiomyopathy, dilated, 1G - autosomal dominant
- OMIM:608807 Muscular dystrophy, limb-girdle, autosomal recessive 10 - autosomal recessive
- OMIM:611705 Salih myopathy - autosomal recessive
- OMIM:613765 Cardiomyopathy, familial hypertrophic, 9 - autosomal dominant
- ORPHA:154 Familial isolated dilated cardiomyopathy - autosomal dominant
- ORPHA:169186 Autosomal recessive centronuclear myopathy - autosomal recessive
- ORPHA:178464 Hereditary myopathy with early respiratory failure - autosomal dominant
- ORPHA:324604 Classic multiminicore myopathy - unknown
- ORPHA:609 Tibial muscular dystrophy - autosomal dominant
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.512
Phenotype Score: 0.434
Variant Score: 0.961
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.434 to ORPHA:169186 Autosomal recessive centronuclear myopathy
- Transcripts:
- TTN:ENST00000342175.6:c.75089G>A:p.(Arg25030His)
- TTN:ENST00000342992.6:c.94004G>A:p.(Arg31335His)
- TTN:ENST00000359218.5:c.74888G>A:p.(Arg24963His)
- TTN:ENST00000460472.2:c.74513G>A:p.(Arg24838His)
- TTN:ENST00000589042.1:c.101708G>A:p.(Arg33903His)
- TTN:ENST00000591111.1:c.96785G>A:p.(Arg32262His)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.999 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- 1000Genomes: 0.0599%
- TOPMed: 0.0091%
- UK10K: 0.0132%
- ExAC AFR: 0.0103%
- ExAC EAS: 0.1759%
- ExAC FIN: 0.0606%
- ExAC NFE: 0.0075%
- ExAC SAS: 0.0061%
- gnomAD_E_AFR: 0.0066%
- gnomAD_E_EAS: 0.1916%
- gnomAD_E_FIN: 0.0767%
- gnomAD_E_NFE: 0.0072%
- gnomAD_E_SAS: 0.0033%
- gnomAD_G_AFR: 0.0114%
- gnomAD_G_EAS: 0.1870%
- gnomAD_G_FIN: 0.0859%
- gnomAD_G_NFE: 0.0067%
- Transcripts:
- TTN:ENST00000342175.6:c.5902A>G:p.(Thr1968Ala)
- TTN:ENST00000342992.6:c.6040A>G:p.(Thr2014Ala)
- TTN:ENST00000359218.5:c.5902A>G:p.(Thr1968Ala)
- TTN:ENST00000360870.5:c.6040A>G:p.(Thr2014Ala)
- TTN:ENST00000460472.2:c.5902A>G:p.(Thr1968Ala)
- TTN:ENST00000589042.1:c.6040A>G:p.(Thr2014Ala)
- TTN:ENST00000591111.1:c.6040A>G:p.(Thr2014Ala)
- Pathogenicity Data:
- Best Score: 0.979328
- Polyphen2: 0.741 (P)
- Mutation Taster: 0.979 (P)
- SIFT: 0.176 (T)
- Frequency Data:
- 1000Genomes: 0.0599%
- TOPMed: 0.0053%
- ExAC EAS: 0.1850%
- gnomAD_E_EAS: 0.1913%
- gnomAD_G_EAS: 0.1856%
- Pathogenicity Data:
- Best Score: 0.999995
- Polyphen2: 0.287 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.934 (T)
- Frequency Data:
- TOPMed: 0.0129%
- ExAC EAS: 0.1857%
- gnomAD_E_EAS: 0.1914%
- gnomAD_E_SAS: 0.0033%
- gnomAD_G_EAS: 0.3141%
- Transcripts:
- TTN:ENST00000342175.6:c.2092G>A:p.(Ala698Thr)
- TTN:ENST00000342992.6:c.2230G>A:p.(Ala744Thr)
- TTN:ENST00000359218.5:c.2092G>A:p.(Ala698Thr)
- TTN:ENST00000360870.5:c.2230G>A:p.(Ala744Thr)
- TTN:ENST00000460472.2:c.2092G>A:p.(Ala698Thr)
- TTN:ENST00000589042.1:c.2230G>A:p.(Ala744Thr)
- TTN:ENST00000591111.1:c.2230G>A:p.(Ala744Thr)
- Pathogenicity Data:
- Best Score: 0.10699999
- Polyphen2: 0.001 (B)
- SIFT: 0.893 (T)
- Frequency Data:
- 1000Genomes: 0.1198%
- TOPMed: 0.0279%
- ExAC EAS: 0.3722%
- ExAC NFE: 0.0045%
- ExAC SAS: 0.0545%
- gnomAD_E_EAS: 0.3951%
- gnomAD_E_FIN: 0.0045%
- gnomAD_E_NFE: 0.0072%
- gnomAD_E_OTH: 0.0182%
- gnomAD_E_SAS: 0.0520%
- gnomAD_G_EAS: 0.3086%
- gnomAD_G_NFE: 0.0133%
- Proximity score 0.517 in interactome to CHST11 and phenotypic similarity 0.832 to ?Osteochondrodysplasia, brachydactyly, and overlapping malformed digits associated with CHST11.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009778, Short thumb
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
- Proximity score 0.517 in interactome to CHST11 and phenotypic similarity 0.716 to mouse mutant of CHST11.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0005306, abnormal phalanx morphology
- HP:0001363, Craniosynostosis - MP:0000440, domed cranium
- HP:0011304, Broad thumb - MP:0005306, abnormal phalanx morphology
- HP:0010055, Broad hallux - MP:0005109, abnormal talus morphology
- Known diseases:
- OMIM:143200 Wagner syndrome 1 - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.512
Phenotype Score: 0.517
Variant Score: 0.867
- Pathogenicity Data:
- Best Score: 0.875
- Polyphen2: 0.028 (B)
- SIFT: 0.125 (T)
- Frequency Data:
- TOPMed: 0.0011%
- ExAC EAS: 0.0231%
- ExAC NFE: 0.0015%
- gnomAD_E_EAS: 0.0174%
- gnomAD_E_NFE: 0.0009%
- gnomAD_G_EAS: 0.0617%
- Proximity score 0.520 in interactome to ZMIZ1 and phenotypic similarity 0.869 to Non-specific syndromic intellectual disability associated with ZMIZ1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010109, Short hallux
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0011304, Broad thumb
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
- Known diseases:
- OMIM:176807 Prostate cancer, susceptibility to (susceptibility)
- OMIM:300068 Androgen insensitivity - X-linked recessive
- OMIM:300633 Hypospadias 1, X-linked - X-linked recessive
- OMIM:312300 Androgen insensitivity, partial, with or without breast cancer - X-linked recessive
- OMIM:313200 Spinal and bulbar muscular atrophy of Kennedy - X-linked recessive
- ORPHA:481 Kennedy disease - X-linked recessive
- ORPHA:90797 Partial androgen insensitivity syndrome - X-linked recessive
- ORPHA:95706 Non-syndromic posterior hypospadias - X-linked recessive
- ORPHA:99429 Complete androgen insensitivity syndrome - X-linked recessive
X_RECESSIVE
Exomiser Score: 0.482
Phenotype Score: 0.520
Variant Score: 0.850
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
X_DOMINANT
Exomiser Score: 0.059
Phenotype Score: 0.260
Variant Score: 0.850
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.513 to Congenital hypotonia, epilepsy, developmental delay, and digital anomalies associated with ATN1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010557, Overlapping fingers
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0010557, Overlapping fingers
- HP:0010055, Broad hallux - HP:0001845, Overlapping toe
- Phenotypic similarity 0.297 to mouse mutant involving ATN1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001289, persistence of hyaloid vascular system
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.502 in interactome to RERE and phenotypic similarity 0.667 to 1p36 deletion syndrome associated with RERE.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0000270, Delayed cranial suture closure
- HP:0011304, Broad thumb - HP:0100490, Camptodactyly of finger
- HP:0010055, Broad hallux - HP:0001829, Foot polydactyly
- Proximity score 0.502 in interactome to RERE and phenotypic similarity 0.280 to mouse mutant of RERE.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0003425, abnormal optic vesicle formation
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.502 in interactome to RERE and phenotypic similarity 0.285 to fish mutant of RERE.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - ZP:0001963, Meckel's cartilage sloped downward, abnormal
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Known diseases:
- OMIM:125370 Dentatorubral-pallidoluysian atrophy - autosomal dominant
- OMIM:618494 Congenital hypotonia, epilepsy, developmental delay, and digital anomalies - autosomal dominant
- ORPHA:101 Dentatorubral pallidoluysian atrophy - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.462
Phenotype Score: 0.513
Variant Score: 0.850
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.513 to OMIM:618494 Congenital hypotonia, epilepsy, developmental delay, and digital anomalies
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.054
Phenotype Score: 0.251
Variant Score: 0.850
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.772 to Weill-Marchesani syndrome 1, recessive associated with ADAMTS10.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0002682, Broad skull
- HP:0011304, Broad thumb - HP:0009768, Broad phalanges of the hand
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Phenotypic similarity 0.512 to mouse mutant involving ADAMTS10.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0003055, abnormal long bone epiphyseal plate morphology
- HP:0001363, Craniosynostosis - MP:0014176, abnormal cilary zonule morphology
- HP:0011304, Broad thumb - MP:0003055, abnormal long bone epiphyseal plate morphology
- HP:0010055, Broad hallux - MP:0003055, abnormal long bone epiphyseal plate morphology
- Proximity score 0.506 in interactome to FBN1 and phenotypic similarity 0.750 to Weill-Marchesani syndrome 2, dominant associated with FBN1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0002682, Broad skull
- HP:0011304, Broad thumb - HP:0009768, Broad phalanges of the hand
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Proximity score 0.506 in interactome to FBN1 and phenotypic similarity 0.683 to mouse mutant of FBN1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0004634, short metacarpal bones
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002543, brachyphalangia
- HP:0010055, Broad hallux - MP:0004634, short metacarpal bones
- Known diseases:
- OMIM:277600 Weill-Marchesani syndrome 1, recessive - autosomal recessive
- ORPHA:3449 Weill-Marchesani syndrome - autosomal recessive
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.443
Phenotype Score: 0.772
Variant Score: 0.548
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.772 to OMIM:277600 Weill-Marchesani syndrome 1, recessive
- Phenotypic similarity 0.691 to ORPHA:3449 Weill-Marchesani syndrome
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.328 (T)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0011%
- ExAC EAS: 0.0118%
- ExAC SAS: 0.0122%
- gnomAD_E_AFR: 0.0068%
- gnomAD_E_EAS: 0.0349%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_SAS: 0.0065%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
AUTOSOMAL_DOMINANT
Exomiser Score: 0.185
Phenotype Score: 0.256
Variant Score: 0.995
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.328 (T)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0011%
- ExAC EAS: 0.0118%
- ExAC SAS: 0.0122%
- gnomAD_E_AFR: 0.0068%
- gnomAD_E_EAS: 0.0349%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_SAS: 0.0065%
- Proximity score 0.500 in interactome to MAP3K20 and phenotypic similarity 0.382 to Split-foot malformation with mesoaxial polydactyly associated with MAP3K20.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0012725, Cutaneous syndactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0012725, Cutaneous syndactyly
- HP:0010055, Broad hallux - HP:0012725, Cutaneous syndactyly
- Proximity score 0.500 in interactome to MAP3K20 and phenotypic similarity 0.723 to mouse mutant of MAP3K20.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000562, polydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0000562, polydactyly
- HP:0010055, Broad hallux - MP:0000562, polydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.432
Phenotype Score: 0.500
Variant Score: 0.851
- Pathogenicity Data:
- Best Score: 0.851
- Polyphen2: 0.020 (B)
- SIFT: 0.149 (T)
- Frequency Data:
- No frequency data
- Proximity score 0.501 in interactome to CSNK2A1 and phenotypic similarity 0.665 to Okur-Chung neurodevelopmental syndrome associated with CSNK2A1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0030084, Clinodactyly
- HP:0010055, Broad hallux - HP:0030084, Clinodactyly
- Proximity score 0.501 in interactome to CSNK2A1 and phenotypic similarity 0.535 to mouse mutant of CSNK2A1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0005650, abnormal limb bud morphology
- HP:0001363, Craniosynostosis - MP:0011495, abnormal head shape
- HP:0011304, Broad thumb - MP:0005650, abnormal limb bud morphology
- HP:0010055, Broad hallux - MP:0005650, abnormal limb bud morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.431
Phenotype Score: 0.501
Variant Score: 0.850
- Transcripts:
- FBRS:ENST00000356166.6:c.87_92dup:p.(Asp30_Arg31dup)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.541 to X-linked non-syndromic intellectual disability associated with DMD.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0004691, 2-3 toe syndactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0006118, Shortening of all distal phalanges of the fingers
- HP:0010055, Broad hallux - HP:0004691, 2-3 toe syndactyly
- Phenotypic similarity 0.306 to mouse mutant involving DMD.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0010227, decreased quadriceps weight
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0010227, decreased quadriceps weight
- HP:0010055, Broad hallux - MP:0010227, decreased quadriceps weight
- Proximity score 0.504 in interactome to TNNI2 and phenotypic similarity 0.494 to Distal arthrogryposis type 1 associated with TNNI2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010557, Overlapping fingers
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001181, Adducted thumb
- HP:0010055, Broad hallux - HP:0010557, Overlapping fingers
- Proximity score 0.504 in interactome to TNNI2 and phenotypic similarity 0.611 to mouse mutant of TNNI2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0006395, abnormal epiphyseal plate morphology
- HP:0001363, Craniosynostosis - MP:0008273, abnormal intramembranous bone ossification
- HP:0011304, Broad thumb - MP:0004351, short humerus
- HP:0010055, Broad hallux - MP:0006395, abnormal epiphyseal plate morphology
- Known diseases:
- OMIM:300376 Becker muscular dystrophy - X-linked recessive
- OMIM:302045 Cardiomyopathy, dilated, 3B - X-linked
- OMIM:310200 Duchenne muscular dystrophy - X-linked recessive
- ORPHA:154 Familial isolated dilated cardiomyopathy - X-linked
- ORPHA:777 X-linked non-syndromic intellectual disability - X-linked recessive
- ORPHA:98895 Becker muscular dystrophy - X-linked recessive
- ORPHA:98896 Duchenne muscular dystrophy - X-linked recessive
X_RECESSIVE
Exomiser Score: 0.408
Phenotype Score: 0.541
Variant Score: 0.794
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.541 to ORPHA:777 X-linked non-syndromic intellectual disability
- Phenotypic similarity 0.274 to ORPHA:98895 Becker muscular dystrophy
- Phenotypic similarity 0.175 to ORPHA:154 Familial isolated dilated cardiomyopathy
- Pathogenicity Data:
- Best Score: 0.955
- Polyphen2: 0.551 (P)
- SIFT: 0.045 (D)
- Frequency Data:
- 1000Genomes: 0.0530%
- TOPMed: 0.0366%
- ExAC EAS: 0.7258%
- ExAC OTH: 0.1590%
- ExAC SAS: 0.0299%
- gnomAD_E_EAS: 0.8089%
- gnomAD_E_OTH: 0.0248%
- gnomAD_E_SAS: 0.0418%
- gnomAD_G_EAS: 0.6849%
- Phenotypic similarity 0.347 to mouse mutant involving NOS2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0000062, increased bone mineral density
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.375
Phenotype Score: 0.347
Variant Score: 0.998
- Transcripts:
- NOS2:ENST00000313735.6:c.2889-2A>C:p.?
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- Frequency Data:
- gnomAD_G_NFE: 0.0134%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.258
Phenotype Score: 0.347
Variant Score: 0.939
- Transcripts:
- NOS2:ENST00000313735.6:c.2889-2A>C:p.?
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- Frequency Data:
- gnomAD_G_NFE: 0.0134%
- Transcripts:
- NOS2:ENST00000313735.6:c.2891C>T:p.(Ala964Val)
- Pathogenicity Data:
- Best Score: 0.88
- Polyphen2: 0.006 (B)
- Mutation Taster: 0.587
- SIFT: 0.120 (T)
- Frequency Data:
- gnomAD_G_NFE: 0.0067%
- Proximity score 0.506 in interactome to SH3PXD2B and phenotypic similarity 0.653 to Frank-Ter Haar syndrome associated with SH3PXD2B.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0100490, Camptodactyly of finger
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Proximity score 0.506 in interactome to SH3PXD2B and phenotypic similarity 0.694 to mouse mutant of SH3PXD2B.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0030853, abnormal iliac crest morphology
- HP:0001363, Craniosynostosis - MP:0003843, abnormal sagittal suture morphology
- HP:0011304, Broad thumb - MP:0000159, abnormal xiphoid process morphology
- HP:0010055, Broad hallux - MP:0030853, abnormal iliac crest morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.372
Phenotype Score: 0.506
Variant Score: 0.817
- Transcripts:
- PAK6:ENST00000260404.4:c.679G>T:p.(Ala227Ser)
- PAK6:ENST00000441369.1:c.679G>T:p.(Ala227Ser)
- PAK6:ENST00000453867.1:c.679G>T:p.(Ala227Ser)
- PAK6:ENST00000455577.2:c.679G>T:p.(Ala227Ser)
- PAK6:ENST00000542403.2:c.679G>T:p.(Ala227Ser)
- PAK6:ENST00000560346.1:c.679G>T:p.(Ala227Ser)
- PAK6:ENST00000558658.1:c.*477G>T:p.(=)
- Pathogenicity Data:
- Best Score: 0.827
- Polyphen2: 0.002 (B)
- SIFT: 0.173 (T)
- Frequency Data:
- TOPMed: 0.0023%
- ExAC EAS: 0.0841%
- gnomAD_E_EAS: 0.0584%
- Proximity score 0.518 in interactome to NABP2 and phenotypic similarity 0.692 to mouse mutant of NABP2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000565, oligodactyly
- HP:0001363, Craniosynostosis - MP:0000438, abnormal cranium morphology
- HP:0011304, Broad thumb - MP:0000565, oligodactyly
- HP:0010055, Broad hallux - MP:0000565, oligodactyly
- Known diseases:
- ORPHA:520 Acute promyelocytic leukemia (unconfirmed)
AUTOSOMAL_DOMINANT
Exomiser Score: 0.364
Phenotype Score: 0.518
Variant Score: 0.800
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.303 to mouse mutant involving RGR.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0005253, abnormal eye physiology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.511 in interactome to RDH10 and phenotypic similarity 0.880 to mouse mutant of RDH10.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002544, brachydactyly
- HP:0001363, Craniosynostosis - MP:0001286, abnormal eye development
- HP:0011304, Broad thumb - MP:0000564, syndactyly
- HP:0010055, Broad hallux - MP:0000564, syndactyly
- Known diseases:
- OMIM:613769 Retinitis pigmentosa 44 - autosomal dominant/recessive
- ORPHA:791 Retinitis pigmentosa - autosomal dominant/recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.348
Phenotype Score: 0.511
Variant Score: 0.800
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
- Proximity score 0.511 in interactome to EVX2 and phenotypic similarity 0.952 to mouse mutant of EVX2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002544, brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002543, brachyphalangia
- HP:0010055, Broad hallux - MP:0002544, brachydactyly
- Known diseases:
- OMIM:201400 Adrenocorticotropic hormone deficiency - autosomal recessive
- ORPHA:199296 Congenital isolated ACTH deficiency - autosomal recessive
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.348
Phenotype Score: 0.511
Variant Score: 0.800
- Transcripts:
- TBX19:ENST00000367821.3:c.603+6_603+7insGTGTGTGT:p.?
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.512 in interactome to ZC3H8 and phenotypic similarity 0.755 to mouse mutant of ZC3H8.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
X_RECESSIVE
Exomiser Score: 0.332
Phenotype Score: 0.512
Variant Score: 0.791
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0530%
- TOPMed: 0.0042%
- ExAC EAS: 0.0754%
- gnomAD_E_EAS: 0.0762%
X_DOMINANT
Exomiser Score: 0.332
Phenotype Score: 0.512
Variant Score: 0.791
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0530%
- TOPMed: 0.0042%
- ExAC EAS: 0.0754%
- gnomAD_E_EAS: 0.0762%
- Proximity score 0.512 in interactome to DISP1 and phenotypic similarity 0.681 to Holoprosencephaly associated with DISP1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0005469, Flat occiput
- HP:0011304, Broad thumb - HP:0001161, Hand polydactyly
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Proximity score 0.512 in interactome to DISP1 and phenotypic similarity 0.568 to mouse mutant of DISP1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000550, abnormal forelimb morphology
- HP:0001363, Craniosynostosis - MP:0011495, abnormal head shape
- HP:0011304, Broad thumb - MP:0000550, abnormal forelimb morphology
- HP:0010055, Broad hallux - MP:0000550, abnormal forelimb morphology
- Proximity score 0.512 in interactome to DISP1 and phenotypic similarity 0.308 to fish mutant of DISP1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - ZP:0005403, joint mandibular arch skeleton malformed, abnormal
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.331
Phenotype Score: 0.512
Variant Score: 0.791
- Transcripts:
- GPC2:ENST00000292377.2:c.1123G>A:p.(Glu375Lys)
- Pathogenicity Data:
- Best Score: 0.791
- Polyphen2: 0.264 (B)
- SIFT: 0.209 (T)
- Frequency Data:
- No frequency data
- Proximity score 0.504 in interactome to EFNB1 and phenotypic similarity 0.807 to Craniofrontonasal dysplasia associated with EFNB1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0004440, Coronal craniosynostosis
- HP:0011304, Broad thumb - HP:0004209, Clinodactyly of the 5th finger
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
- Proximity score 0.504 in interactome to EFNB1 and phenotypic similarity 0.765 to mouse mutant of EFNB1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000562, polydactyly
- HP:0001363, Craniosynostosis - MP:0004378, frontal bone foramen
- HP:0011304, Broad thumb - MP:0000562, polydactyly
- HP:0010055, Broad hallux - MP:0000562, polydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.331
Phenotype Score: 0.504
Variant Score: 0.800
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.505 in interactome to ADK and phenotypic similarity 0.393 to Hypermethioninemia due to adenosine kinase deficiency associated with ADK.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001786, Narrow foot
- HP:0001363, Craniosynostosis - HP:0002007, Frontal bossing
- HP:0011304, Broad thumb - HP:0001786, Narrow foot
- HP:0010055, Broad hallux - HP:0001786, Narrow foot
- Proximity score 0.505 in interactome to ADK and phenotypic similarity 0.755 to mouse mutant of ADK.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
- Known diseases:
- OMIM:619150 Intellectual developmental disorder with paroxysmal dyskinesia or seizures - autosomal recessive
- ORPHA:31709 Infantile convulsions and choreoathetosis - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.331
Phenotype Score: 0.505
Variant Score: 0.799
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
- ESP EA: 0.0116%
- ESP All: 0.0077%
- ExAC NFE: 0.0016%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_NFE: 0.0046%
- Proximity score 0.503 in interactome to PDE6D and phenotypic similarity 0.703 to Orofaciodigital syndrome type 6 associated with PDE6D.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0004422, Biparietal narrowing
- HP:0011304, Broad thumb - HP:0001161, Hand polydactyly
- HP:0010055, Broad hallux - HP:0001829, Foot polydactyly
- Proximity score 0.503 in interactome to PDE6D and phenotypic similarity 0.343 to mouse mutant of PDE6D.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0004022, abnormal cone electrophysiology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Known diseases:
- OMIM:606703 Dyskinesia, familial, with facial myokymia - autosomal dominant
- ORPHA:1429 Benign hereditary chorea - autosomal dominant
- ORPHA:324588 Familial dyskinesia and facial myokymia - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.330
Phenotype Score: 0.503
Variant Score: 0.800
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0004%
- Phenotypic similarity 0.340 to mouse mutant involving RP1L1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0004022, abnormal cone electrophysiology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Known diseases:
- OMIM:613587 Occult macular dystrophy - autosomal dominant
- OMIM:618826 Retinitis pigmentosa 88 - autosomal recessive
- ORPHA:791 Retinitis pigmentosa - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.329
Phenotype Score: 0.340
Variant Score: 0.984
- Transcripts:
- RP1L1:ENST00000382483.3:c.68G>C:p.(Arg23Pro)
- Pathogenicity Data:
- Best Score: 0.994
- SIFT: 0.006 (D)
- Frequency Data:
- gnomAD_E_AFR: 0.0696%
- gnomAD_E_FIN: 0.0515%
- gnomAD_E_NFE: 0.0700%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.227
Phenotype Score: 0.340
Variant Score: 0.929
- Transcripts:
- RP1L1:ENST00000382483.3:c.68G>C:p.(Arg23Pro)
- Pathogenicity Data:
- Best Score: 0.994
- SIFT: 0.006 (D)
- Frequency Data:
- gnomAD_E_AFR: 0.0696%
- gnomAD_E_FIN: 0.0515%
- gnomAD_E_NFE: 0.0700%
- Transcripts:
- RP1L1:ENST00000382483.3:c.3971A>G:p.(Glu1324Gly)
- Pathogenicity Data:
- Best Score: 0.873
- SIFT: 0.127 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.307 to mouse mutant involving CGN.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002111, abnormal tail morphology
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002111, abnormal tail morphology
- HP:0010055, Broad hallux - MP:0002111, abnormal tail morphology
- Proximity score 0.503 in interactome to TGFBR1 and phenotypic similarity 0.749 to Loeys-Dietz syndrome 1 associated with TGFBR1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001166, Arachnodactyly
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0001162, Postaxial hand polydactyly
- HP:0010055, Broad hallux - HP:0001166, Arachnodactyly
- Proximity score 0.503 in interactome to TGFBR1 and phenotypic similarity 0.952 to mouse mutant of TGFBR1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0000081, premature cranial suture closure
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.328
Phenotype Score: 0.503
Variant Score: 0.800
- Transcripts:
- CGN:ENST00000271636.7:c.1897-4C>T:p.?
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0004%
- Proximity score 0.502 in interactome to BMS1 and phenotypic similarity 0.602 to Aplasia cutis congenita associated with BMS1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001770, Toe syndactyly
- HP:0001363, Craniosynostosis - HP:0001362, Calvarial skull defect
- HP:0011304, Broad thumb - HP:0006101, Finger syndactyly
- HP:0010055, Broad hallux - HP:0001770, Toe syndactyly
- Proximity score 0.502 in interactome to BMS1 and phenotypic similarity 0.299 to mouse mutant of BMS1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001303, abnormal lens morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.326
Phenotype Score: 0.502
Variant Score: 0.800
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.501 in interactome to NOS3 and phenotypic similarity 0.712 to mouse mutant of NOS3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000564, syndactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0000564, syndactyly
- HP:0010055, Broad hallux - MP:0000564, syndactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.324
Phenotype Score: 0.501
Variant Score: 0.800
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.245 to mouse mutant involving SEC63.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0010124, decreased bone mineral content
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.501 in interactome to CSNK2A1 and phenotypic similarity 0.665 to Okur-Chung neurodevelopmental syndrome associated with CSNK2A1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0030084, Clinodactyly
- HP:0010055, Broad hallux - HP:0030084, Clinodactyly
- Proximity score 0.501 in interactome to CSNK2A1 and phenotypic similarity 0.535 to mouse mutant of CSNK2A1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0005650, abnormal limb bud morphology
- HP:0001363, Craniosynostosis - MP:0011495, abnormal head shape
- HP:0011304, Broad thumb - MP:0005650, abnormal limb bud morphology
- HP:0010055, Broad hallux - MP:0005650, abnormal limb bud morphology
- Known diseases:
- OMIM:617004 Polycystic liver disease 2 - autosomal dominant
- ORPHA:2924 Isolated polycystic liver disease - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.324
Phenotype Score: 0.501
Variant Score: 0.800
- Transcripts:
- SEC63:ENST00000369002.4:c.1936-9_1936-8insTTT:p.?
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.506 in interactome to EPB41L1 and phenotypic similarity 0.684 to ?Intellectual developmental disorder, autosomal dominant 11 associated with EPB41L1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0002007, Frontal bossing
- HP:0011304, Broad thumb - HP:0001181, Adducted thumb
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Proximity score 0.506 in interactome to EPB41L1 and phenotypic similarity 0.294 to mouse mutant of EPB41L1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001340, abnormal eyelid morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.324
Phenotype Score: 0.506
Variant Score: 0.794
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_G_AFR: 0.0517%
- gnomAD_G_NFE: 0.0235%
- Proximity score 0.500 in interactome to PIGK and phenotypic similarity 0.660 to Neurodevelopmental disorder with hypotonia and cerebellar atrophy, with or without seizures associated with PIGK.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001156, Brachydactyly
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.323
Phenotype Score: 0.500
Variant Score: 0.800
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.303 to mouse mutant involving EYA3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.500 in interactome to MEIS2 and phenotypic similarity 0.856 to Cleft palate, cardiac defects, and mental retardation associated with MEIS2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0009237, Short 5th finger
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0011304, Broad thumb
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
- Proximity score 0.500 in interactome to MEIS2 and phenotypic similarity 0.299 to mouse mutant of MEIS2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001312, abnormal cornea morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.322
Phenotype Score: 0.500
Variant Score: 0.800
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.500 in interactome to COL11A2 and phenotypic similarity 0.660 to Fibrochondrogenesis associated with COL11A2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0001357, Plagiocephaly
- HP:0011304, Broad thumb - HP:0000885, Broad ribs
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Proximity score 0.500 in interactome to COL11A2 and phenotypic similarity 0.502 to mouse mutant of COL11A2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0006397, disorganized long bone epiphyseal plate
- HP:0001363, Craniosynostosis - MP:0030049, prominent forehead
- HP:0011304, Broad thumb - MP:0006397, disorganized long bone epiphyseal plate
- HP:0010055, Broad hallux - MP:0006397, disorganized long bone epiphyseal plate
- Proximity score 0.500 in interactome to COL11A2 and phenotypic similarity 0.447 to fish mutant of COL11A2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - ZP:0000119, endochondral ossification disrupted, abnormal
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.322
Phenotype Score: 0.500
Variant Score: 0.800
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.500 in interactome to TELO2 and phenotypic similarity 0.650 to TELO2-related intellectual disability-neurodevelopmental disorder associated with TELO2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001182, Tapered finger
- HP:0010055, Broad hallux - HP:0004692, 4-5 toe syndactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.322
Phenotype Score: 0.500
Variant Score: 0.800
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0004%
- Proximity score 0.500 in interactome to MOGS and phenotypic similarity 0.479 to Congenital disorder of glycosylation, type IIb associated with MOGS.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010557, Overlapping fingers
- HP:0001363, Craniosynostosis - HP:0000269, Prominent occiput
- HP:0011304, Broad thumb - HP:0010557, Overlapping fingers
- HP:0010055, Broad hallux - HP:0010557, Overlapping fingers
- Proximity score 0.500 in interactome to MOGS and phenotypic similarity 0.920 to mouse mutant of MOGS.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002544, brachydactyly
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb - MP:0002544, brachydactyly
- HP:0010055, Broad hallux - MP:0002544, brachydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.319
Phenotype Score: 0.500
Variant Score: 0.798
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0030%
- ExAC AMR: 0.0173%
- ExAC NFE: 0.0030%
- gnomAD_E_AMR: 0.0149%
- gnomAD_E_NFE: 0.0045%
- gnomAD_G_NFE: 0.0067%
- Proximity score 0.500 in interactome to EXOC8 and phenotypic similarity 0.635 to ?Neurodevelopmental disorder with microcephaly, seizures, and brain atrophy associated with EXOC8.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.316
Phenotype Score: 0.500
Variant Score: 0.797
- Transcripts:
- ARHGAP27:ENST00000376922.2:c.720+8G>A:p.?
- ARHGAP27:ENST00000428638.1:c.1743+8G>A:p.?
- ARHGAP27:ENST00000442348.1:c.1662+8G>A:p.?
- ARHGAP27:ENST00000455881.1:c.720+8G>A:p.?
- ARHGAP27:ENST00000528384.1:c.639+8G>A:p.?
- ARHGAP27:ENST00000532038.1:c.1077+8G>A:p.?
- ARHGAP27:ENST00000532891.2:c.1677+8G>A:p.?
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0038%
- ExAC EAS: 0.0116%
- gnomAD_E_EAS: 0.0058%
- gnomAD_E_NFE: 0.0018%
- gnomAD_G_FIN: 0.0286%
- Proximity score 0.500 in interactome to MOGS and phenotypic similarity 0.479 to Congenital disorder of glycosylation, type IIb associated with MOGS.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010557, Overlapping fingers
- HP:0001363, Craniosynostosis - HP:0000269, Prominent occiput
- HP:0011304, Broad thumb - HP:0010557, Overlapping fingers
- HP:0010055, Broad hallux - HP:0010557, Overlapping fingers
- Proximity score 0.500 in interactome to MOGS and phenotypic similarity 0.920 to mouse mutant of MOGS.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002544, brachydactyly
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb - MP:0002544, brachydactyly
- HP:0010055, Broad hallux - MP:0002544, brachydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.309
Phenotype Score: 0.500
Variant Score: 0.793
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0015%
- ExAC EAS: 0.0347%
- gnomAD_E_EAS: 0.0232%
- gnomAD_G_EAS: 0.0617%
- Phenotypic similarity 0.288 to mouse mutant involving NRG1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001322, abnormal iris morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.501 in interactome to EVX2 and phenotypic similarity 0.952 to mouse mutant of EVX2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002544, brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002543, brachyphalangia
- HP:0010055, Broad hallux - MP:0002544, brachydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.303
Phenotype Score: 0.501
Variant Score: 0.789
- Transcripts:
- NRG1:ENST00000521670.1:c.*21+6G>C:p.(=)
- NRG1:ENST00000287842.3:c.1260-383G>C:p.(=)
- NRG1:ENST00000287845.5:c.1182-383G>C:p.(=)
- NRG1:ENST00000338921.4:c.1293-383G>C:p.(=)
- NRG1:ENST00000356819.4:c.1284-383G>C:p.(=)
- NRG1:ENST00000405005.3:c.1269-383G>C:p.(=)
- NRG1:ENST00000519301.1:c.1119-383G>C:p.(=)
- NRG1:ENST00000539990.1:c.798-383G>C:p.(=)
- NRG1:ENST00000341377.5:c.*584-383G>C:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0026%
- ExAC EAS: 0.0927%
- gnomAD_E_EAS: 0.0871%
- gnomAD_G_EAS: 0.0618%
- Phenotypic similarity 0.332 to Aromatase deficiency associated with CYP19A1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0002857, Genu valgum
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0002857, Genu valgum
- HP:0010055, Broad hallux - HP:0002857, Genu valgum
- Phenotypic similarity 0.352 to mouse mutant involving CYP19A1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.504 in interactome to SC5D and phenotypic similarity 0.646 to Lathosterolosis associated with SC5D.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001770, Toe syndactyly
- HP:0001363, Craniosynostosis - HP:0005487, Prominent metopic ridge
- HP:0011304, Broad thumb - HP:0001162, Postaxial hand polydactyly
- HP:0010055, Broad hallux - HP:0001770, Toe syndactyly
- Proximity score 0.504 in interactome to SC5D and phenotypic similarity 0.731 to mouse mutant of SC5D.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000564, syndactyly
- HP:0001363, Craniosynostosis - MP:0002639, micrognathia
- HP:0011304, Broad thumb - MP:0000564, syndactyly
- HP:0010055, Broad hallux - MP:0000564, syndactyly
- Known diseases:
- OMIM:139300 Aromatase excess syndrome - autosomal dominant
- OMIM:613546 Aromatase deficiency - autosomal recessive
- ORPHA:91 Aromatase deficiency - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.302
Phenotype Score: 0.504
Variant Score: 0.786
- Transcripts:
- CYP19A1:ENST00000260433.2:c.577C>T:p.(Arg193Cys)
- CYP19A1:ENST00000396402.1:c.577C>T:p.(Arg193Cys)
- CYP19A1:ENST00000396404.4:c.577C>T:p.(Arg193Cys)
- CYP19A1:ENST00000405913.3:c.577C>T:p.(Arg193Cys)
- CYP19A1:ENST00000557858.1:c.577C>T:p.(Arg193Cys)
- CYP19A1:ENST00000559878.1:c.577C>T:p.(Arg193Cys)
- Pathogenicity Data:
- Best Score: 0.78617
- Polyphen2: 0.001 (B)
- Mutation Taster: 0.786
- SIFT: 0.252 (T)
- Frequency Data:
- TOPMed: 0.0011%
- ExAC NFE: 0.0015%
- gnomAD_E_NFE: 0.0018%
- Phenotypic similarity 0.314 to mouse mutant involving ZSCAN2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0004609, vertebral fusion
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.301
Phenotype Score: 0.314
Variant Score: 1.000
- Transcripts:
- ZSCAN2:ENST00000327179.6:c.692G>C:p.(Ser231Thr)
- ZSCAN2:ENST00000358472.3:c.245G>C:p.(Ser82Thr)
- ZSCAN2:ENST00000448803.2:c.695G>C:p.(Ser232Thr)
- ZSCAN2:ENST00000546148.1:c.695G>C:p.(Ser232Thr)
- ZSCAN2:ENST00000485222.2:c.577+118G>C:p.(=)
- ZSCAN2:ENST00000538076.1:c.577+118G>C:p.(=)
- ZSCAN2:ENST00000541040.1:c.577+118G>C:p.(=)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.094 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.226 (T)
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.464 to Arthrogryposis multiplex congenita 3, myogenic type associated with SYNE1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001181, Adducted thumb
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001181, Adducted thumb
- HP:0010055, Broad hallux - HP:0001181, Adducted thumb
- Phenotypic similarity 0.305 to mouse mutant involving SYNE1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0009434, paraparesis
- HP:0001363, Craniosynostosis - MP:0001852, conjunctivitis
- HP:0011304, Broad thumb - MP:0009434, paraparesis
- HP:0010055, Broad hallux - MP:0009434, paraparesis
- Known diseases:
- OMIM:610743 Spinocerebellar ataxia, autosomal recessive 8 - autosomal recessive
- OMIM:612998 Emery-Dreifuss muscular dystrophy 4, autosomal dominant - autosomal dominant
- OMIM:618484 Arthrogryposis multiplex congenita 3, myogenic type - autosomal recessive
- ORPHA:88644 Autosomal recessive ataxia, Beauce type - autosomal recessive
- ORPHA:98853 Autosomal dominant Emery-Dreifuss muscular dystrophy - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.288
Phenotype Score: 0.315
Variant Score: 0.991
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.315 to ORPHA:98853 Autosomal dominant Emery-Dreifuss muscular dystrophy
- Pathogenicity Data:
- Best Score: 0.999954
- Polyphen2: 0.074 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.041 (D)
- Frequency Data:
- TOPMed: 0.0135%
- ESP EA: 0.0116%
- ESP All: 0.0077%
- ExAC AMR: 0.0086%
- ExAC EAS: 0.0347%
- ExAC NFE: 0.0060%
- ExAC SAS: 0.0061%
- gnomAD_E_AMR: 0.0060%
- gnomAD_E_EAS: 0.0464%
- gnomAD_E_NFE: 0.0063%
- gnomAD_E_SAS: 0.0032%
- gnomAD_G_EAS: 0.0617%
- gnomAD_G_NFE: 0.0067%
- Proximity score 0.501 in interactome to MOGS and phenotypic similarity 0.479 to Congenital disorder of glycosylation, type IIb associated with MOGS.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010557, Overlapping fingers
- HP:0001363, Craniosynostosis - HP:0000269, Prominent occiput
- HP:0011304, Broad thumb - HP:0010557, Overlapping fingers
- HP:0010055, Broad hallux - HP:0010557, Overlapping fingers
- Proximity score 0.501 in interactome to MOGS and phenotypic similarity 0.920 to mouse mutant of MOGS.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002544, brachydactyly
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb - MP:0002544, brachydactyly
- HP:0010055, Broad hallux - MP:0002544, brachydactyly
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.285
Phenotype Score: 0.501
Variant Score: 0.780
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.002 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.110 (T)
- Frequency Data:
- 1000Genomes: 0.0599%
- TOPMed: 0.0143%
- ExAC EAS: 0.1041%
- gnomAD_E_EAS: 0.1160%
- gnomAD_G_EAS: 0.0617%
- Pathogenicity Data:
- Best Score: 0.999988
- Polyphen2: 0.006 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.274 (T)
- Frequency Data:
- 1000Genomes: 0.3395%
- TOPMed: 0.0521%
- ExAC EAS: 1.2133%
- ExAC NFE: 0.0030%
- gnomAD_E_EAS: 1.2757%
- gnomAD_E_NFE: 0.0036%
- gnomAD_E_OTH: 0.0182%
- gnomAD_E_SAS: 0.0032%
- gnomAD_G_EAS: 1.4180%
- Phenotypic similarity 0.275 to mouse mutant involving RGPD4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0004021, abnormal rod electrophysiology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.504 in interactome to GRIP1 and phenotypic similarity 0.584 to Fraser syndrome associated with GRIP1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001770, Toe syndactyly
- HP:0001363, Craniosynostosis - HP:0001362, Calvarial skull defect
- HP:0011304, Broad thumb - HP:0006101, Finger syndactyly
- HP:0010055, Broad hallux - HP:0001770, Toe syndactyly
- Proximity score 0.504 in interactome to GRIP1 and phenotypic similarity 0.757 to mouse mutant of GRIP1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000562, polydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0000562, polydactyly
- HP:0010055, Broad hallux - MP:0000562, polydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.282
Phenotype Score: 0.504
Variant Score: 0.775
- Pathogenicity Data:
- Best Score: 0.778
- Polyphen2: 0.000 (B)
- SIFT: 0.222 (T)
- Frequency Data:
- gnomAD_E_EAS: 0.0295%
- gnomAD_E_FIN: 0.0045%
- gnomAD_E_NFE: 0.0028%
- gnomAD_E_OTH: 0.0187%
- gnomAD_E_SAS: 0.0177%
- gnomAD_G_NFE: 0.0153%
- Phenotypic similarity 0.295 to mouse mutant involving GBP3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001303, abnormal lens morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.262
Phenotype Score: 0.295
Variant Score: 1.000
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.124
Phenotype Score: 0.295
Variant Score: 0.900
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- GBP3:ENST00000370481.4:c.426G>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.294 to mouse mutant involving TMEM145.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001304, cataract
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.253
Phenotype Score: 0.294
Variant Score: 0.996
- Transcripts:
- TMEM145:ENST00000301204.3:c.1280C>G:p.(Pro427Arg)
- Pathogenicity Data:
- Best Score: 0.997535
- Polyphen2: 0.675 (P)
- Mutation Taster: 0.998 (P)
- SIFT: 0.428 (T)
- Frequency Data:
- ExAC EAS: 0.0116%
- gnomAD_E_EAS: 0.0058%
- Phenotypic similarity 0.314 to mouse mutant involving GOLGA8T.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0004609, vertebral fusion
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.249
Phenotype Score: 0.314
Variant Score: 0.972
- Transcripts:
- GOLGA8K:ENST00000512626.2:c.931C>G:p.(Leu311Val)
- Pathogenicity Data:
- Best Score: 0.976
- Mutation Taster: 0.506
- SIFT: 0.024 (D)
- Frequency Data:
- gnomAD_G_FIN: 0.0306%
- gnomAD_G_NFE: 0.0081%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.005
Phenotype Score: 0.314
Variant Score: 0.521
- Transcripts:
- GOLGA8K:ENST00000512626.2:c.931C>G:p.(Leu311Val)
- Pathogenicity Data:
- Best Score: 0.976
- Mutation Taster: 0.506
- SIFT: 0.024 (D)
- Frequency Data:
- gnomAD_G_FIN: 0.0306%
- gnomAD_G_NFE: 0.0081%
- Transcripts:
- GOLGA8K:ENST00000512626.2:c.1623C>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_G_AFR: 1.1773%
- gnomAD_G_AMR: 0.7788%
- gnomAD_G_EAS: 0.5426%
- gnomAD_G_FIN: 0.4038%
- gnomAD_G_NFE: 0.5090%
- gnomAD_G_OTH: 0.4087%
- Phenotypic similarity 0.275 to mouse mutant involving C11orf54.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0011960, abnormal eye anterior chamber depth
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.223
Phenotype Score: 0.275
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- Frequency Data:
- TOPMed: 0.0004%
- Proximity score 0.500 in interactome to GRHL2 and phenotypic similarity 0.347 to Ectodermal dysplasia/short stature syndrome associated with GRHL2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0008404, Nail dystrophy
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0008404, Nail dystrophy
- HP:0010055, Broad hallux - HP:0008404, Nail dystrophy
- Proximity score 0.500 in interactome to GRHL2 and phenotypic similarity 0.756 to mouse mutant of GRHL2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000564, syndactyly
- HP:0001363, Craniosynostosis - MP:0011495, abnormal head shape
- HP:0011304, Broad thumb - MP:0000564, syndactyly
- HP:0010055, Broad hallux - MP:0000564, syndactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.196
Phenotype Score: 0.500
Variant Score: 0.727
- Transcripts:
- URB1:ENST00000382751.3:c.5693G>A:p.(Arg1898His)
- Pathogenicity Data:
- Best Score: 0.728
- Polyphen2: 0.000 (B)
- SIFT: 0.272 (T)
- Frequency Data:
- TOPMed: 0.0008%
- gnomAD_E_AMR: 0.0042%
- gnomAD_E_NFE: 0.0035%
- gnomAD_G_NFE: 0.0067%
- Phenotypic similarity 0.667 to 1p36 deletion syndrome associated with KCNAB2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0000270, Delayed cranial suture closure
- HP:0011304, Broad thumb - HP:0100490, Camptodactyly of finger
- HP:0010055, Broad hallux - HP:0001829, Foot polydactyly
- Proximity score 0.505 in interactome to KCNH1 and phenotypic similarity 0.856 to Temple-Baraitser syndrome associated with KCNH1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010055, Broad hallux
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0011304, Broad thumb
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
- Known diseases - observed variants incompatible with mode of inheritance:
- ORPHA:1606 1p36 deletion syndrome (CNV)
AUTOSOMAL_DOMINANT
Exomiser Score: 0.186
Phenotype Score: 0.253
Variant Score: 1.000
- Transcripts:
- KCNAB2:ENST00000378087.3:c.437A>G:p.(Gln146Arg)
- KCNAB2:ENST00000378111.1:c.437A>G:p.(Gln146Arg)
- KCNAB2:ENST00000164247.1:c.*1359A>G:p.(=)
- KCNAB2:ENST00000341524.1:c.*1359A>G:p.(=)
- KCNAB2:ENST00000352527.1:c.*1359A>G:p.(=)
- KCNAB2:ENST00000378083.3:c.*1359A>G:p.(=)
- KCNAB2:ENST00000378097.1:c.*1359A>G:p.(=)
- Pathogenicity Data:
- Best Score: 1.0
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.185
Phenotype Score: 0.253
Variant Score: 1.000
- Transcripts:
- KCNAB2:ENST00000378087.3:c.437A>G:p.(Gln146Arg)
- KCNAB2:ENST00000378111.1:c.437A>G:p.(Gln146Arg)
- KCNAB2:ENST00000164247.1:c.*1359A>G:p.(=)
- KCNAB2:ENST00000341524.1:c.*1359A>G:p.(=)
- KCNAB2:ENST00000352527.1:c.*1359A>G:p.(=)
- KCNAB2:ENST00000378083.3:c.*1359A>G:p.(=)
- KCNAB2:ENST00000378097.1:c.*1359A>G:p.(=)
- Pathogenicity Data:
- Best Score: 1.0
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- Transcripts:
- KCNAB2:ENST00000378087.3:c.436C>T:p.(Gln146*)
- KCNAB2:ENST00000378111.1:c.436C>T:p.(Gln146*)
- KCNAB2:ENST00000164247.1:c.*1358C>T:p.(=)
- KCNAB2:ENST00000341524.1:c.*1358C>T:p.(=)
- KCNAB2:ENST00000352527.1:c.*1358C>T:p.(=)
- KCNAB2:ENST00000378083.3:c.*1358C>T:p.(=)
- KCNAB2:ENST00000378097.1:c.*1358C>T:p.(=)
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- Frequency Data:
- gnomAD_E_NFE: 0.0038%
- Phenotypic similarity 0.275 to mouse mutant involving ITPR3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001314, corneal opacity
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.505 in interactome to INPP5K and phenotypic similarity 0.631 to Marinesco-Sjögren syndrome associated with INPP5K.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0010508, Metatarsus valgus
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:222100 Diabetes, type 1, susceptibility to (susceptibility)
AUTOSOMAL_DOMINANT
Exomiser Score: 0.186
Phenotype Score: 0.253
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 0.999998
- Polyphen2: 0.825 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.006 (D)
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.473 to Microcephaly 16, primary, autosomal recessive associated with ANKLE2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001181, Adducted thumb
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001181, Adducted thumb
- HP:0010055, Broad hallux - HP:0001181, Adducted thumb
- Phenotypic similarity 0.244 to mouse mutant involving ANKLE2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0002792, abnormal retinal vasculature morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.504 in interactome to LEMD2 and phenotypic similarity 0.629 to Marbach-Rustad progeroid syndrome associated with LEMD2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0031846, Femur fracture
- HP:0001363, Craniosynostosis - HP:0002645, Wormian bones
- HP:0011304, Broad thumb - HP:0031846, Femur fracture
- HP:0010055, Broad hallux - HP:0031846, Femur fracture
- Proximity score 0.504 in interactome to LEMD2 and phenotypic similarity 0.257 to mouse mutant of LEMD2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0006069, abnormal retinal neuronal layer morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:616681 Microcephaly 16, primary, autosomal recessive - autosomal recessive
- ORPHA:2512 Autosomal recessive primary microcephaly - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.185
Phenotype Score: 0.252
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.958 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.021 (D)
- Frequency Data:
- No frequency data
- Proximity score 0.502 in interactome to HDAC4 and phenotypic similarity 0.656 to 2q37 microdeletion syndrome associated with HDAC4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0002007, Frontal bossing
- HP:0011304, Broad thumb - HP:0006101, Finger syndactyly
- HP:0010055, Broad hallux - HP:0001770, Toe syndactyly
- Proximity score 0.502 in interactome to HDAC4 and phenotypic similarity 0.934 to mouse mutant of HDAC4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000165, abnormal long bone hypertrophic chondrocyte zone
- HP:0001363, Craniosynostosis - MP:0030356, premature lambdoid suture closure
- HP:0011304, Broad thumb - MP:0000165, abnormal long bone hypertrophic chondrocyte zone
- HP:0010055, Broad hallux - MP:0000165, abnormal long bone hypertrophic chondrocyte zone
- Proximity score 0.502 in interactome to HDAC4 and phenotypic similarity 0.614 to fish mutant of HDAC4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - ZP:0107238, anguloarticular premature ossification, abnormal
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:209920 MHC class II deficiency, complementation group B - autosomal recessive
- ORPHA:572 Immunodeficiency by defective expression of MHC class II - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.183
Phenotype Score: 0.251
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.995 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.026 (D)
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.620 to Osteogenesis imperfecta, type VII associated with CRTAP.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0002979, Bowing of the legs
- HP:0001363, Craniosynostosis - HP:0002645, Wormian bones
- HP:0011304, Broad thumb - HP:0002812, Coxa vara
- HP:0010055, Broad hallux - HP:0002979, Bowing of the legs
- Phenotypic similarity 0.491 to mouse mutant involving CRTAP.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0006397, disorganized long bone epiphyseal plate
- HP:0001363, Craniosynostosis - MP:0002896, abnormal bone mineralization
- HP:0011304, Broad thumb - MP:0006397, disorganized long bone epiphyseal plate
- HP:0010055, Broad hallux - MP:0006397, disorganized long bone epiphyseal plate
- Proximity score 0.500 in interactome to DDR2 and phenotypic similarity 0.612 to Spondylometaepiphyseal dysplasia, short limb-hand type associated with DDR2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0006009, Broad phalanx
- HP:0001363, Craniosynostosis - HP:0002007, Frontal bossing
- HP:0011304, Broad thumb - HP:0009875, Triangular shaped distal phalanges of the hand
- HP:0010055, Broad hallux - HP:0006009, Broad phalanx
- Proximity score 0.500 in interactome to DDR2 and phenotypic similarity 0.515 to mouse mutant of DDR2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0006395, abnormal epiphyseal plate morphology
- HP:0001363, Craniosynostosis - MP:0000438, abnormal cranium morphology
- HP:0011304, Broad thumb - MP:0006395, abnormal epiphyseal plate morphology
- HP:0010055, Broad hallux - MP:0006395, abnormal epiphyseal plate morphology
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:610682 Osteogenesis imperfecta, type VII - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.182
Phenotype Score: 0.250
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.991 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.004 (D)
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.479 to Primary ciliary dyskinesia associated with CCDC40.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001217, Clubbing
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001217, Clubbing
- HP:0010055, Broad hallux - HP:0001217, Clubbing
- Proximity score 0.500 in interactome to RNF113A and phenotypic similarity 0.712 to Trichothiodystrophy associated with RNF113A.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001217, Clubbing
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0001217, Clubbing
- HP:0010055, Broad hallux - HP:0001217, Clubbing
- Proximity score 0.500 in interactome to RNF113A and phenotypic similarity 0.262 to mouse mutant of RNF113A.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0002792, abnormal retinal vasculature morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:613808 Ciliary dyskinesia, primary, 15 - autosomal recessive
- ORPHA:244 Primary ciliary dyskinesia - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.182
Phenotype Score: 0.250
Variant Score: 1.000
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.322 to mouse mutant involving PCDH15.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0000062, increased bone mineral density
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.500 in interactome to HS2ST1 and phenotypic similarity 0.703 to Neurofacioskeletal syndrome with or without renal agenesis associated with HS2ST1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0011927, Short digit
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009836, Broad distal phalanx of finger
- HP:0010055, Broad hallux - HP:0010186, Broad distal phalanx of the toes
- Proximity score 0.500 in interactome to HS2ST1 and phenotypic similarity 0.698 to mouse mutant of HS2ST1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000562, polydactyly
- HP:0001363, Craniosynostosis - MP:0002896, abnormal bone mineralization
- HP:0011304, Broad thumb - MP:0000562, polydactyly
- HP:0010055, Broad hallux - MP:0000562, polydactyly
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:601067 Usher syndrome, type 1D/F digenic - autosomal recessive
- OMIM:602083 Usher syndrome, type 1F - autosomal recessive
- OMIM:609533 Deafness, autosomal recessive 23 - autosomal recessive
- ORPHA:231169 Usher syndrome type 1 - autosomal recessive
- ORPHA:231169 Usher syndrome type 1 - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.182
Phenotype Score: 0.250
Variant Score: 1.000
- Transcripts:
- PCDH15:ENST00000320301.6:c.1744A>G:p.(Thr582Ala)
- PCDH15:ENST00000361849.3:c.1744A>G:p.(Thr582Ala)
- PCDH15:ENST00000373955.1:c.1744A>G:p.(Thr582Ala)
- PCDH15:ENST00000373957.3:c.1678A>G:p.(Thr560Ala)
- PCDH15:ENST00000373965.2:c.1765A>G:p.(Thr589Ala)
- PCDH15:ENST00000395430.1:c.1744A>G:p.(Thr582Ala)
- PCDH15:ENST00000395432.2:c.1633A>G:p.(Thr545Ala)
- PCDH15:ENST00000395433.1:c.1678A>G:p.(Thr560Ala)
- PCDH15:ENST00000395438.1:c.1744A>G:p.(Thr582Ala)
- PCDH15:ENST00000395445.1:c.1765A>G:p.(Thr589Ala)
- PCDH15:ENST00000395446.1:c.1744A>G:p.(Thr582Ala)
- PCDH15:ENST00000409834.1:c.577A>G:p.(Thr193Ala)
- PCDH15:ENST00000414778.1:c.1759A>G:p.(Thr587Ala)
- PCDH15:ENST00000437009.1:c.1744A>G:p.(Thr582Ala)
- PCDH15:ENST00000395440.1:c.1305+42543A>G:p.(=)
- PCDH15:ENST00000395442.1:c.1098+60796A>G:p.(=)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.999 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.002 (D)
- Frequency Data:
- No frequency data
- Proximity score 0.500 in interactome to GDF5 and phenotypic similarity 0.832 to Brachydactyly, type A2 associated with GDF5.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0009536, Short 2nd finger
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009182, Triangular shaped middle phalanx of the 5th finger
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
- Proximity score 0.500 in interactome to GDF5 and phenotypic similarity 0.911 to mouse mutant of GDF5.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002544, brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002544, brachydactyly
- HP:0010055, Broad hallux - MP:0002544, brachydactyly
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:615112 Urofacial syndrome 2 - autosomal recessive
- ORPHA:2704 Ochoa syndrome - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.182
Phenotype Score: 0.250
Variant Score: 1.000
- Transcripts:
- LRIG2:ENST00000361127.5:c.1105A>C:p.(Asn369His)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 1.000 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.001 (D)
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.271 to mouse mutant involving MGME1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0003795, abnormal bone structure
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.500 in interactome to SNRPN and phenotypic similarity 0.664 to Prader-Willi syndrome due to translocation associated with SNRPN.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0005469, Flat occiput
- HP:0011304, Broad thumb - HP:0004209, Clinodactyly of the 5th finger
- HP:0010055, Broad hallux - HP:0001845, Overlapping toe
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:615084 Mitochondrial DNA depletion syndrome 11 - autosomal recessive
- ORPHA:352447 Progressive external ophthalmoplegia-myopathy-emaciation syndrome - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.182
Phenotype Score: 0.250
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.997 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.002 (D)
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.334 to mouse mutant involving TTLL5.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0002864, abnormal ocular fundus morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.500 in interactome to RXRA and phenotypic similarity 0.772 to mouse mutant of RXRA.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis - MP:0002092, abnormal eye morphology
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
- Known diseases:
- OMIM:615860 Cone-rod dystrophy 19 - autosomal recessive
- ORPHA:1872 Cone rod dystrophy - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.176
Phenotype Score: 0.250
Variant Score: 0.996
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.961 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.004 (D)
- Frequency Data:
- TOPMed: 0.0057%
- ExAC AMR: 0.0173%
- ExAC NFE: 0.0075%
- ExAC SAS: 0.0121%
- gnomAD_E_AFR: 0.0065%
- gnomAD_E_AMR: 0.0060%
- gnomAD_E_NFE: 0.0054%
- gnomAD_E_SAS: 0.0065%
- gnomAD_G_AFR: 0.0115%
- gnomAD_G_FIN: 0.0286%
- gnomAD_G_NFE: 0.0067%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.041
Phenotype Score: 0.500
Variant Score: 0.538
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.961 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.004 (D)
- Frequency Data:
- TOPMed: 0.0057%
- ExAC AMR: 0.0173%
- ExAC NFE: 0.0075%
- ExAC SAS: 0.0121%
- gnomAD_E_AFR: 0.0065%
- gnomAD_E_AMR: 0.0060%
- gnomAD_E_NFE: 0.0054%
- gnomAD_E_SAS: 0.0065%
- gnomAD_G_AFR: 0.0115%
- gnomAD_G_FIN: 0.0286%
- gnomAD_G_NFE: 0.0067%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.3594%
- TOPMed: 0.0642%
- ESP EA: 0.0349%
- ESP All: 0.0231%
- ExAC EAS: 0.9373%
- ExAC FIN: 0.5897%
- ExAC NFE: 0.0959%
- ExAC OTH: 0.5507%
- ExAC SAS: 0.1272%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_EAS: 0.9047%
- gnomAD_E_FIN: 0.4172%
- gnomAD_E_NFE: 0.0422%
- gnomAD_E_OTH: 0.3648%
- gnomAD_E_SAS: 0.1300%
- gnomAD_G_EAS: 0.7398%
- gnomAD_G_FIN: 0.6297%
- gnomAD_G_NFE: 0.0866%
- gnomAD_G_OTH: 0.3055%
- Proximity score 0.500 in interactome to DPH1 and phenotypic similarity 0.740 to Developmental delay with short stature, dysmorphic facial features, and sparse hair associated with DPH1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001800, Hypoplastic toenails
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0001800, Hypoplastic toenails
- HP:0010055, Broad hallux - HP:0001800, Hypoplastic toenails
- Proximity score 0.500 in interactome to DPH1 and phenotypic similarity 0.739 to mouse mutant of DPH1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0009743, preaxial polydactyly
- HP:0001363, Craniosynostosis - MP:0002116, abnormal craniofacial bone morphology
- HP:0011304, Broad thumb - MP:0009743, preaxial polydactyly
- HP:0010055, Broad hallux - MP:0009743, preaxial polydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.158
Phenotype Score: 0.500
Variant Score: 0.699
- Pathogenicity Data:
- Best Score: 0.699
- Polyphen2: 0.006 (B)
- SIFT: 0.301 (T)
- Frequency Data:
- TOPMed: 0.0011%
- Proximity score 0.506 in interactome to STAMBP and phenotypic similarity 0.666 to Microcephaly-capillary malformation syndrome associated with STAMBP.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009882, Short distal phalanx of finger
- HP:0010055, Broad hallux - HP:0030084, Clinodactyly
- Proximity score 0.506 in interactome to STAMBP and phenotypic similarity 0.268 to mouse mutant of STAMBP.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001344, blepharoptosis
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Known diseases:
- OMIM:219090 Pituitary adenoma 4, ACTH-secreting, somatic - autosomal dominant/recessive
- ORPHA:96253 Cushing disease (unconfirmed)
AUTOSOMAL_DOMINANT
Exomiser Score: 0.149
Phenotype Score: 0.506
Variant Score: 0.685
- Pathogenicity Data:
- Best Score: 0.685
- Polyphen2: 0.006 (B)
- SIFT: 0.315 (T)
- Frequency Data:
- No frequency data
- Proximity score 0.503 in interactome to GKN2 and phenotypic similarity 0.935 to mouse mutant of GKN2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002544, brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002544, brachydactyly
- HP:0010055, Broad hallux - MP:0002544, brachydactyly
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.144
Phenotype Score: 0.503
Variant Score: 0.683
- Transcripts:
- MUC6:ENST00000421673.2:c.6068C>A:p.(Thr2023Lys)
- Pathogenicity Data:
- Best Score: 0.948
- Polyphen2: 0.005 (B)
- SIFT: 0.052 (D)
- Frequency Data:
- 1000Genomes: 0.0399%
- TOPMed: 0.0399%
- gnomAD_G_AFR: 0.2420%
- gnomAD_G_EAS: 0.1190%
- gnomAD_G_FIN: 1.0045%
- gnomAD_G_NFE: 0.3645%
- gnomAD_G_OTH: 0.5000%
- Transcripts:
- MUC6:ENST00000421673.2:c.1453+4C>T:p.?
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.1198%
- TOPMed: 0.0574%
- ExAC AFR: 0.0103%
- ExAC AMR: 0.0087%
- ExAC EAS: 0.9061%
- ExAC NFE: 0.0030%
- ExAC SAS: 0.0303%
- gnomAD_E_AFR: 0.0066%
- gnomAD_E_AMR: 0.0089%
- gnomAD_E_EAS: 0.8935%
- gnomAD_E_NFE: 0.0036%
- gnomAD_E_SAS: 0.0292%
- gnomAD_G_EAS: 0.6790%
AUTOSOMAL_DOMINANT
Exomiser Score: 0.025
Phenotype Score: 0.503
Variant Score: 0.479
- Transcripts:
- MUC6:ENST00000421673.2:c.5615T>C:p.(Met1872Thr)
- Pathogenicity Data:
- Best Score: 0.481
- Polyphen2: 0.094 (B)
- SIFT: 0.519 (T)
- Frequency Data:
- gnomAD_E_FIN: 0.0149%
- gnomAD_E_NFE: 0.0026%
- gnomAD_E_OTH: 0.0286%
- Transcripts:
- MUC6:ENST00000421673.2:c.6087C>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- MUC6:ENST00000421673.2:c.5331C>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- MUC6:ENST00000421673.2:c.5601C>G:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_NFE: 0.0020%
- Transcripts:
- MUC6:ENST00000421673.2:c.5640G>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0206%
- gnomAD_E_AMR: 0.0041%
- gnomAD_E_EAS: 0.0102%
- gnomAD_E_FIN: 0.0066%
- gnomAD_E_NFE: 0.0106%
- gnomAD_E_OTH: 0.0258%
- gnomAD_E_SAS: 0.0080%
- Transcripts:
- MUC6:ENST00000421673.2:c.4968G>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.7955%
- gnomAD_E_AMR: 0.0549%
- gnomAD_E_EAS: 0.1312%
- gnomAD_E_FIN: 0.1639%
- gnomAD_E_NFE: 0.0564%
- gnomAD_E_OTH: 0.0898%
- gnomAD_E_SAS: 0.0475%
- Transcripts:
- MUC6:ENST00000421673.2:c.6069A>G:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0399%
- TOPMed: 0.0399%
- gnomAD_G_AFR: 0.2656%
- gnomAD_G_EAS: 0.1220%
- gnomAD_G_FIN: 0.9091%
- gnomAD_G_NFE: 0.3708%
- gnomAD_G_OTH: 0.5025%
- Phenotypic similarity 0.331 to mouse mutant involving FOXK2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.501 in interactome to SIN3A and phenotypic similarity 0.696 to 15q24 microdeletion syndrome associated with SIN3A.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009623, Proximal placement of thumb
- HP:0010055, Broad hallux - HP:0001780, Abnormality of toe
AUTOSOMAL_DOMINANT
Exomiser Score: 0.143
Phenotype Score: 0.501
Variant Score: 0.686
- Transcripts:
- FOXK2:ENST00000335255.5:c.1771G>A:p.(Gly591Ser)
- Pathogenicity Data:
- Best Score: 0.69
- Polyphen2: 0.011 (B)
- SIFT: 0.310 (T)
- Frequency Data:
- TOPMed: 0.0144%
- ExAC AFR: 0.0098%
- ExAC AMR: 0.0087%
- ExAC EAS: 0.0463%
- ExAC NFE: 0.0228%
- ExAC SAS: 0.0303%
- gnomAD_E_AFR: 0.0066%
- gnomAD_E_AMR: 0.0238%
- gnomAD_E_EAS: 0.0464%
- gnomAD_E_NFE: 0.0252%
- gnomAD_E_OTH: 0.0183%
- gnomAD_E_SAS: 0.0260%
- gnomAD_G_AFR: 0.0343%
- Phenotypic similarity 0.396 to mouse mutant involving SVEP1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002109, abnormal limb morphology
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002109, abnormal limb morphology
- HP:0010055, Broad hallux - MP:0002109, abnormal limb morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.139
Phenotype Score: 0.396
Variant Score: 0.800
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.507 in interactome to B4GALT7 and phenotypic similarity 0.696 to Ehlers-Danlos syndrome, spondylodysplastic type, 1 associated with B4GALT7.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0011308, Slender toe
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0006243, Phalangeal dislocation
- HP:0010055, Broad hallux - HP:0011308, Slender toe
- Proximity score 0.507 in interactome to B4GALT7 and phenotypic similarity 0.328 to fish mutant of B4GALT7.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - ZP:0001049, head circular, abnormal
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.137
Phenotype Score: 0.507
Variant Score: 0.673
- Pathogenicity Data:
- Best Score: 0.918
- Polyphen2: 0.007 (B)
- SIFT: 0.082 (T)
- Frequency Data:
- gnomAD_G_AFR: 0.0435%
- gnomAD_G_FIN: 0.3147%
- gnomAD_G_NFE: 0.0077%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_G_AFR: 0.1590%
- gnomAD_G_AMR: 0.9328%
- gnomAD_G_EAS: 0.0914%
- gnomAD_G_FIN: 0.6334%
- gnomAD_G_NFE: 0.0320%
- gnomAD_G_OTH: 0.1359%
- Pathogenicity Data:
- Best Score: 0.908
- Polyphen2: 0.051 (B)
- SIFT: 0.092 (T)
- Frequency Data:
- gnomAD_G_AFR: 0.2225%
- gnomAD_G_AMR: 1.7110%
- gnomAD_G_EAS: 0.5144%
- gnomAD_G_FIN: 0.8319%
- gnomAD_G_NFE: 0.0496%
- gnomAD_G_OTH: 0.1475%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC NFE: 0.0124%
- gnomAD_E_NFE: 0.0061%
- gnomAD_G_AFR: 0.0441%
- gnomAD_G_FIN: 0.1923%
- Phenotypic similarity 0.551 to Alström syndrome associated with ALMS1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001831, Short toe
- HP:0001363, Craniosynostosis - HP:0004438, Hyperostosis frontalis interna
- HP:0011304, Broad thumb - HP:0009381, Short finger
- HP:0010055, Broad hallux - HP:0001831, Short toe
- Phenotypic similarity 0.298 to mouse mutant involving ALMS1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001326, retinal degeneration
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.503 in interactome to SDCCAG8 and phenotypic similarity 0.504 to Bardet-Biedl syndrome associated with SDCCAG8.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0006101, Finger syndactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001162, Postaxial hand polydactyly
- HP:0010055, Broad hallux - HP:0006101, Finger syndactyly
- Proximity score 0.503 in interactome to SDCCAG8 and phenotypic similarity 0.737 to mouse mutant of SDCCAG8.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000562, polydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0000562, polydactyly
- HP:0010055, Broad hallux - MP:0000562, polydactyly
- Known diseases:
- OMIM:203800 Alstrom syndrome - autosomal recessive
- ORPHA:64 Alström syndrome - autosomal recessive
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.131
Phenotype Score: 0.551
Variant Score: 0.617
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.551 to ORPHA:64 Alström syndrome
- Phenotypic similarity 0.383 to OMIM:203800 Alstrom syndrome
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.1997%
- TOPMed: 0.0495%
- ExAC AFR: 0.0102%
- ExAC AMR: 0.0087%
- ExAC EAS: 0.7655%
- ExAC OTH: 0.2222%
- ExAC SAS: 0.0242%
- gnomAD_E_AFR: 0.0131%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_EAS: 0.7713%
- gnomAD_E_OTH: 0.0549%
- gnomAD_E_SAS: 0.0260%
- gnomAD_G_AFR: 0.0458%
- gnomAD_G_EAS: 1.2979%
- gnomAD_G_OTH: 0.1018%
AUTOSOMAL_DOMINANT
Exomiser Score: 0.054
Phenotype Score: 0.252
Variant Score: 0.850
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.500 in interactome to USP12 and phenotypic similarity 0.737 to mouse mutant of USP12.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000565, oligodactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0000565, oligodactyly
- HP:0010055, Broad hallux - MP:0000565, oligodactyly
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:300066 Deafness, X-linked 4 - X-linked dominant
X_RECESSIVE
Exomiser Score: 0.127
Phenotype Score: 0.250
Variant Score: 0.954
- Transcripts:
- SMPX:ENST00000379494.3:c.55A>G:p.(Asn19Asp)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.986 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- TOPMed: 0.0064%
- ExAC EAS: 0.1816%
- ExAC OTH: 0.1587%
- gnomAD_E_EAS: 0.2410%
- gnomAD_G_EAS: 0.2904%
- Phenotypic similarity 0.667 to 1p36 deletion syndrome associated with HSPG2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0000270, Delayed cranial suture closure
- HP:0011304, Broad thumb - HP:0100490, Camptodactyly of finger
- HP:0010055, Broad hallux - HP:0001829, Foot polydactyly
- Phenotypic similarity 0.701 to mouse mutant involving HSPG2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0006397, disorganized long bone epiphyseal plate
- HP:0001363, Craniosynostosis - MP:0030029, wide cranial sutures
- HP:0011304, Broad thumb - MP:0006397, disorganized long bone epiphyseal plate
- HP:0010055, Broad hallux - MP:0006397, disorganized long bone epiphyseal plate
- Proximity score 0.510 in interactome to HS6ST1 and phenotypic similarity 0.332 to Hypogonadotropic hypogonadism 15 with or without anosmia associated with HS6ST1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0002857, Genu valgum
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0002857, Genu valgum
- HP:0010055, Broad hallux - HP:0002857, Genu valgum
- Proximity score 0.510 in interactome to HS6ST1 and phenotypic similarity 0.783 to mouse mutant of HS6ST1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0005306, abnormal phalanx morphology
- HP:0001363, Craniosynostosis - MP:0002092, abnormal eye morphology
- HP:0011304, Broad thumb - MP:0005306, abnormal phalanx morphology
- HP:0010055, Broad hallux - MP:0005104, abnormal tarsal bone morphology
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:224410 Dyssegmental dysplasia, Silverman-Handmaker type - autosomal recessive
- OMIM:255800 Schwartz-Jampel syndrome, type 1 - autosomal recessive
- ORPHA:1606 1p36 deletion syndrome (CNV)
- ORPHA:1865 Dyssegmental dysplasia, Silverman-Handmaker type - autosomal recessive
- ORPHA:800 Schwartz-Jampel syndrome - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.116
Phenotype Score: 0.350
Variant Score: 0.829
- Pathogenicity Data:
- Best Score: 0.838
- Polyphen2: 0.018 (B)
- SIFT: 0.162 (T)
- Frequency Data:
- 1000Genomes: 0.0399%
- TOPMed: 0.0104%
- ExAC EAS: 0.0466%
- gnomAD_E_EAS: 0.0755%
- gnomAD_E_NFE: 0.0009%
- gnomAD_G_EAS: 0.0617%
- Phenotypic similarity 0.326 to mouse mutant involving FADS6.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001289, persistence of hyaloid vascular system
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.109
Phenotype Score: 0.326
Variant Score: 0.850
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.500 in interactome to DOCK3 and phenotypic similarity 0.869 to Non-specific syndromic intellectual disability associated with DOCK3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010109, Short hallux
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0011304, Broad thumb
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.109
Phenotype Score: 0.500
Variant Score: 0.651
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- Frequency Data:
- gnomAD_E_AFR: 0.0136%
- gnomAD_E_AMR: 0.0061%
- gnomAD_E_EAS: 0.0060%
- gnomAD_E_NFE: 0.0027%
- gnomAD_E_SAS: 0.0033%
- gnomAD_G_AFR: 0.3301%
- gnomAD_G_AMR: 0.7102%
- gnomAD_G_EAS: 0.5691%
- gnomAD_G_FIN: 0.4237%
- gnomAD_G_NFE: 0.2110%
- gnomAD_G_OTH: 0.2451%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0275%
- gnomAD_E_AMR: 0.0138%
- gnomAD_E_EAS: 0.0061%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_OTH: 0.0194%
- gnomAD_E_SAS: 0.0110%
- gnomAD_G_AFR: 0.6667%
- gnomAD_G_AMR: 1.3678%
- gnomAD_G_EAS: 0.8772%
- gnomAD_G_FIN: 1.4587%
- gnomAD_G_NFE: 0.4727%
- gnomAD_G_OTH: 0.5249%
- Phenotypic similarity 0.503 to Trismus-pseudocamptodactyly syndrome associated with MYH8.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010621, Cutaneous syndactyly of toes
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001840, Metatarsus adductus
- HP:0010055, Broad hallux - HP:0001765, Hammertoe
- Proximity score 0.506 in interactome to RABL2B and phenotypic similarity 0.752 to mouse mutant of RABL2B.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis - MP:0006203, eye hemorrhage
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
- Known diseases:
- OMIM:158300 Trismus-pseudocamptodactyly syndrome - autosomal dominant
- OMIM:608837 Carney complex variant - autosomal dominant
- ORPHA:3377 Trismus-pseudocamptodactyly syndrome - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.092
Phenotype Score: 0.506
Variant Score: 0.625
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.503 to OMIM:158300 Trismus-pseudocamptodactyly syndrome
- Phenotypic similarity 0.452 to ORPHA:3377 Trismus-pseudocamptodactyly syndrome
- Transcripts:
- MYH8:ENST00000403437.2:c.2741A>C:p.(Asn914Thr)
- Pathogenicity Data:
- Best Score: 0.626
- Polyphen2: 0.000 (B)
- SIFT: 0.374 (T)
- Frequency Data:
- TOPMed: 0.0011%
- ExAC EAS: 0.0116%
- gnomAD_E_EAS: 0.0174%
- Phenotypic similarity 0.494 to Distal arthrogryposis type 1 associated with TNNI2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010557, Overlapping fingers
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001181, Adducted thumb
- HP:0010055, Broad hallux - HP:0010557, Overlapping fingers
- Phenotypic similarity 0.611 to mouse mutant involving TNNI2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0006395, abnormal epiphyseal plate morphology
- HP:0001363, Craniosynostosis - MP:0008273, abnormal intramembranous bone ossification
- HP:0011304, Broad thumb - MP:0004351, short humerus
- HP:0010055, Broad hallux - MP:0006395, abnormal epiphyseal plate morphology
- Proximity score 0.503 in interactome to MYH3 and phenotypic similarity 0.728 to Contractures, pterygia, and spondylocarpostarsal fusion syndrome 1A associated with MYH3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0008368, Tarsal synostosis
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0009702, Carpal synostosis
- HP:0010055, Broad hallux - HP:0008368, Tarsal synostosis
- Known diseases:
- OMIM:601680 Arthrogryposis, distal, type 2B1 - autosomal dominant
- ORPHA:1146 Distal arthrogryposis type 1 - autosomal dominant
- ORPHA:1147 Sheldon-Hall syndrome - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.090
Phenotype Score: 0.611
Variant Score: 0.503
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.494 to ORPHA:1146 Distal arthrogryposis type 1
- Phenotypic similarity 0.478 to ORPHA:1147 Sheldon-Hall syndrome
- Phenotypic similarity 0.417 to OMIM:601680 Arthrogryposis, distal, type 2B1
- Pathogenicity Data:
- Best Score: 0.504
- Polyphen2: 0.073 (B)
- SIFT: 0.496 (T)
- Frequency Data:
- TOPMed: 0.0015%
- ExAC EAS: 0.0118%
- ExAC NFE: 0.0016%
- gnomAD_E_EAS: 0.0174%
- Proximity score 0.502 in interactome to NUP188 and phenotypic similarity 0.609 to Sandestig-Stefanova syndrome associated with NUP188.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0030084, Clinodactyly
- HP:0001363, Craniosynostosis - HP:0005487, Prominent metopic ridge
- HP:0011304, Broad thumb - HP:0030084, Clinodactyly
- HP:0010055, Broad hallux - HP:0030084, Clinodactyly
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.086
Phenotype Score: 0.502
Variant Score: 0.621
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0144%
- ESP AA: 0.7501%
- ESP EA: 0.5937%
- ESP All: 0.6470%
- ExAC AFR: 0.2414%
- ExAC AMR: 0.3114%
- ExAC EAS: 0.4309%
- ExAC FIN: 0.1362%
- ExAC NFE: 0.3920%
- ExAC OTH: 0.5531%
- ExAC SAS: 0.6689%
- gnomAD_E_AFR: 0.0333%
- gnomAD_E_AMR: 0.0061%
- gnomAD_E_EAS: 0.0239%
- gnomAD_E_FIN: 0.0282%
- gnomAD_E_NFE: 0.0184%
- gnomAD_E_SAS: 0.0134%
- gnomAD_G_AFR: 0.0345%
- gnomAD_G_NFE: 0.0134%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.1198%
- TOPMed: 0.1198%
- ESP AA: 1.0080%
- ESP EA: 1.0177%
- ESP All: 1.0144%
- ExAC AFR: 0.4176%
- ExAC AMR: 0.1745%
- ExAC EAS: 1.1193%
- ExAC FIN: 0.0157%
- ExAC NFE: 0.8665%
- ExAC OTH: 0.8621%
- ExAC SAS: 0.3222%
- gnomAD_E_AFR: 0.0460%
- gnomAD_E_AMR: 0.1459%
- gnomAD_E_EAS: 1.2767%
- gnomAD_E_FIN: 0.0461%
- gnomAD_E_NFE: 0.0631%
- gnomAD_E_OTH: 0.1893%
- gnomAD_E_SAS: 0.1594%
- gnomAD_G_EAS: 0.5703%
- gnomAD_G_FIN: 0.0515%
- gnomAD_G_NFE: 0.0392%
- gnomAD_G_OTH: 0.1370%
- Phenotypic similarity 0.375 to mouse mutant involving CD36.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0003664, ocular pterygium
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.505 in interactome to THBS3 and phenotypic similarity 0.694 to mouse mutant of THBS3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000559, abnormal femur morphology
- HP:0001363, Craniosynostosis - MP:0003416, premature bone ossification
- HP:0011304, Broad thumb - MP:0000559, abnormal femur morphology
- HP:0010055, Broad hallux - MP:0000559, abnormal femur morphology
- Known diseases:
- OMIM:608404 Platelet glycoprotein IV deficiency - autosomal recessive
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.074
Phenotype Score: 0.505
Variant Score: 0.601
- Transcripts:
- CD36:ENST00000309881.7:c.1163A>T:p.(Gln388Leu)
- CD36:ENST00000394788.3:c.1163A>T:p.(Gln388Leu)
- CD36:ENST00000432207.1:c.1163A>T:p.(Gln388Leu)
- CD36:ENST00000433696.2:c.1046A>T:p.(Gln349Leu)
- CD36:ENST00000435819.1:c.1163A>T:p.(Gln388Leu)
- CD36:ENST00000447544.2:c.1163A>T:p.(Gln388Leu)
- CD36:ENST00000534394.1:c.935A>T:p.(Gln312Leu)
- CD36:ENST00000538969.1:c.983A>T:p.(Gln328Leu)
- CD36:ENST00000544133.1:c.*108A>T:p.(=)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 1.000 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- 1000Genomes: 0.0399%
- TOPMed: 0.0144%
- ExAC EAS: 0.6437%
- gnomAD_E_EAS: 0.5500%
- gnomAD_E_OTH: 0.0184%
- gnomAD_G_EAS: 0.7453%
- Transcripts:
- CD36:ENST00000309881.7:c.1228_1239del:p.(Ile410_Ile413del)
- CD36:ENST00000394788.3:c.1228_1239del:p.(Ile410_Ile413del)
- CD36:ENST00000432207.1:c.1228_1239del:p.(Ile410_Ile413del)
- CD36:ENST00000433696.2:c.1111_1122del:p.(Ile371_Ile374del)
- CD36:ENST00000435819.1:c.1228_1239del:p.(Ile410_Ile413del)
- CD36:ENST00000447544.2:c.1228_1239del:p.(Ile410_Ile413del)
- CD36:ENST00000534394.1:c.1000_1011del:p.(Ile334_Ile337del)
- CD36:ENST00000538969.1:c.1048_1059del:p.(Ile350_Ile353del)
- CD36:ENST00000544133.1:c.*173_*184del:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.1597%
- TOPMed: 0.0457%
- gnomAD_E_EAS: 1.0669%
- gnomAD_E_OTH: 0.0183%
- gnomAD_G_EAS: 1.6749%
- Proximity score 0.500 in interactome to ZMPSTE24 and phenotypic similarity 0.646 to Mandibuloacral dysplasia with type B lipodystrophy associated with ZMPSTE24.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0009803, Short phalanx of finger
- HP:0001363, Craniosynostosis - HP:0002645, Wormian bones
- HP:0011304, Broad thumb - HP:0009803, Short phalanx of finger
- HP:0010055, Broad hallux - HP:0001870, Acroosteolysis of distal phalanges (feet)
- Proximity score 0.500 in interactome to ZMPSTE24 and phenotypic similarity 0.679 to mouse mutant of ZMPSTE24.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000558, abnormal tibia morphology
- HP:0001363, Craniosynostosis - MP:0002835, abnormal cranial suture morphology
- HP:0011304, Broad thumb - MP:0000558, abnormal tibia morphology
- HP:0010055, Broad hallux - MP:0000558, abnormal tibia morphology
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.065
Phenotype Score: 0.500
Variant Score: 0.591
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- Frequency Data:
- TOPMed: 0.0076%
- ESP AA: 0.0227%
- ESP EA: 0.0116%
- ESP All: 0.0154%
- ExAC AFR: 0.0096%
- ExAC EAS: 0.0693%
- ExAC NFE: 0.0120%
- gnomAD_E_AFR: 0.0065%
- gnomAD_E_EAS: 0.0812%
- gnomAD_E_NFE: 0.0098%
- gnomAD_E_SAS: 0.0032%
- gnomAD_G_EAS: 0.1235%
- Pathogenicity Data:
- Best Score: 0.959
- Polyphen2: 0.003 (B)
- SIFT: 0.041 (D)
- Frequency Data:
- 1000Genomes: 0.1398%
- TOPMed: 0.1730%
- ExAC AFR: 0.0194%
- ExAC AMR: 1.9247%
- ExAC EAS: 1.1477%
- ExAC NFE: 0.0075%
- ExAC SAS: 0.0122%
- gnomAD_E_AFR: 0.0131%
- gnomAD_E_AMR: 1.7037%
- gnomAD_E_EAS: 1.1608%
- gnomAD_E_NFE: 0.0045%
- gnomAD_E_OTH: 0.1278%
- gnomAD_E_SAS: 0.0098%
- gnomAD_G_AFR: 0.0115%
- gnomAD_G_AMR: 1.5513%
- gnomAD_G_EAS: 1.1728%
- gnomAD_G_OTH: 0.2041%
- Proximity score 0.500 in interactome to SCLT1 and phenotypic similarity 0.720 to mouse mutant of SCLT1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0009743, preaxial polydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0009743, preaxial polydactyly
- HP:0010055, Broad hallux - MP:0009743, preaxial polydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.058
Phenotype Score: 0.500
Variant Score: 0.577
- Transcripts:
- OR3A1:ENST00000323404.1:c.824A>G:p.(Lys275Arg)
- Pathogenicity Data:
- Best Score: 0.579
- Polyphen2: 0.344 (B)
- SIFT: 0.421 (T)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0011%
- ExAC EAS: 0.0116%
- gnomAD_E_EAS: 0.0058%
- Proximity score 0.504 in interactome to POGZ and phenotypic similarity 0.707 to White-Sutton syndrome associated with POGZ.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0000248, Brachycephaly
- HP:0011304, Broad thumb - HP:0001156, Brachydactyly
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
X_RECESSIVE
Exomiser Score: 0.057
Phenotype Score: 0.504
Variant Score: 0.570
- Transcripts:
- ZNF280C:ENST00000370978.4:c.2159A>G:p.(Asn720Ser)
- Pathogenicity Data:
- Best Score: 0.866
- Polyphen2: 0.022 (B)
- SIFT: 0.134 (T)
- Frequency Data:
- 1000Genomes: 0.1325%
- TOPMed: 0.0665%
- ExAC EAS: 1.0749%
- ExAC NFE: 0.0042%
- ExAC SAS: 0.0103%
- gnomAD_E_EAS: 1.1985%
- gnomAD_E_NFE: 0.0026%
- gnomAD_E_SAS: 0.0119%
- gnomAD_G_EAS: 1.2597%
- Phenotypic similarity 0.262 to mouse mutant involving ALDH1L2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001325, abnormal retina morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.503 in interactome to SHMT2 and phenotypic similarity 0.669 to Neurodevelopmental disorder with cardiomyopathy, spasticity, and brain abnormalities associated with SHMT2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0004691, 2-3 toe syndactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009943, Complete duplication of thumb phalanx
- HP:0010055, Broad hallux - HP:0004691, 2-3 toe syndactyly
- Proximity score 0.503 in interactome to SHMT2 and phenotypic similarity 0.262 to mouse mutant of SHMT2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0008259, abnormal optic disk morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.054
Phenotype Score: 0.503
Variant Score: 0.566
- Pathogenicity Data:
- Best Score: 0.571
- Polyphen2: 0.016 (B)
- SIFT: 0.429 (T)
- Frequency Data:
- ExAC EAS: 0.0347%
- gnomAD_E_EAS: 0.0464%
- gnomAD_G_EAS: 0.0617%
- Phenotypic similarity 0.551 to Congenital muscular dystrophy, Ullrich type associated with COL6A2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001238, Slender finger
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001181, Adducted thumb
- HP:0010055, Broad hallux - HP:0010511, Long toe
- Known diseases:
- OMIM:158810 Bethlem myopathy 1 - autosomal dominant/recessive
- OMIM:254090 Ullrich congenital muscular dystrophy 1 - autosomal dominant/recessive
- OMIM:255600 ?Myosclerosis, congenital (unconfirmed)
- ORPHA:610 Bethlem myopathy - autosomal dominant/recessive
- ORPHA:75840 Congenital muscular dystrophy, Ullrich type - autosomal dominant/recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.049
Phenotype Score: 0.551
Variant Score: 0.502
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.551 to ORPHA:75840 Congenital muscular dystrophy, Ullrich type
- Phenotypic similarity 0.475 to ORPHA:610 Bethlem myopathy
- Phenotypic similarity 0.396 to OMIM:158810 Bethlem myopathy 1
- Phenotypic similarity 0.324 to OMIM:254090 Ullrich congenital muscular dystrophy 1
- Pathogenicity Data:
- Best Score: 0.502
- Polyphen2: 0.001 (B)
- SIFT: 0.498 (T)
- Frequency Data:
- gnomAD_E_NFE: 0.0009%
- Phenotypic similarity 0.265 to mouse mutant involving NLRP7.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0005543, decreased cornea thickness
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:231090 Hydatidiform mole, recurrent, 1 - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.045
Phenotype Score: 0.133
Variant Score: 0.965
- Transcripts:
- NLRP7:ENST00000328092.5:c.1258G>A:p.(Ala420Thr)
- NLRP7:ENST00000340844.2:c.1258G>A:p.(Ala420Thr)
- NLRP7:ENST00000446217.1:c.1342G>A:p.(Ala448Thr)
- NLRP7:ENST00000448121.2:c.1258G>A:p.(Ala420Thr)
- NLRP7:ENST00000588756.1:c.1258G>A:p.(Ala420Thr)
- NLRP7:ENST00000590030.1:c.1258G>A:p.(Ala420Thr)
- NLRP7:ENST00000592784.1:c.1258G>A:p.(Ala420Thr)
- Pathogenicity Data:
- Best Score: 0.973
- Polyphen2: 0.901 (P)
- SIFT: 0.027 (D)
- Frequency Data:
- TOPMed: 0.0008%
- ExAC EAS: 0.0362%
- gnomAD_E_EAS: 0.0409%
- gnomAD_G_EAS: 0.0620%
- Phenotypic similarity 0.320 to mouse mutant involving FSD2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0002092, abnormal eye morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.044
Phenotype Score: 0.320
Variant Score: 0.748
- Pathogenicity Data:
- Best Score: 0.753977
- Polyphen2: 0.005 (B)
- Mutation Taster: 0.754
- SIFT: 0.513 (T)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0072%
- ESP AA: 0.0544%
- ESP All: 0.0168%
- ExAC AFR: 0.0102%
- ExAC AMR: 0.0086%
- ExAC EAS: 0.0232%
- ExAC NFE: 0.0015%
- gnomAD_E_AFR: 0.0065%
- gnomAD_E_AMR: 0.0060%
- gnomAD_E_EAS: 0.0116%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_OTH: 0.0183%
- Phenotypic similarity 0.559 to Phelan-McDermid syndrome associated with SHANK3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0004691, 2-3 toe syndactyly
- HP:0001363, Craniosynostosis - HP:0000268, Dolichocephaly
- HP:0011304, Broad thumb - HP:0004209, Clinodactyly of the 5th finger
- HP:0010055, Broad hallux - HP:0004691, 2-3 toe syndactyly
- Phenotypic similarity 0.548 to mouse mutant involving SHANK3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000572, abnormal autopod morphology
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0000572, abnormal autopod morphology
- HP:0010055, Broad hallux - MP:0000572, abnormal autopod morphology
- Proximity score 0.507 in interactome to RABL2B and phenotypic similarity 0.752 to mouse mutant of RABL2B.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis - MP:0006203, eye hemorrhage
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:606232 Phelan-McDermid syndrome - autosomal dominant
- OMIM:613950 Schizophrenia 15 (susceptibility)
- ORPHA:48652 Monosomy 22q13.3 (CNV)
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.043
Phenotype Score: 0.274
Variant Score: 0.800
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.505 in interactome to BRIP1 and phenotypic similarity 0.676 to Fanconi anemia associated with BRIP1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001770, Toe syndactyly
- HP:0001363, Craniosynostosis - HP:0000268, Dolichocephaly
- HP:0011304, Broad thumb - HP:0001199, Triphalangeal thumb
- HP:0010055, Broad hallux - HP:0001770, Toe syndactyly
- Proximity score 0.505 in interactome to BRIP1 and phenotypic similarity 0.275 to mouse mutant of BRIP1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001304, cataract
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Known diseases:
- OMIM:614337 Colorectal cancer, hereditary nonpolyposis, type 4 - autosomal dominant
- OMIM:619101 Mismatch repair cancer syndrome 4 - autosomal recessive
- ORPHA:144 Lynch syndrome - autosomal dominant
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.042
Phenotype Score: 0.505
Variant Score: 0.535
- Pathogenicity Data:
- Best Score: 0.999977
- Polyphen2: 0.997 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.218 (T)
- Frequency Data:
- gnomAD_E_AMR: 0.0388%
- gnomAD_E_NFE: 0.0371%
- gnomAD_E_OTH: 0.0549%
- gnomAD_E_SAS: 0.0098%
- gnomAD_G_AFR: 0.0582%
- gnomAD_G_EAS: 0.1880%
- gnomAD_G_FIN: 0.0291%
- gnomAD_G_NFE: 0.1291%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC NFE: 0.0047%
- gnomAD_E_AFR: 0.0198%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_EAS: 0.0058%
- gnomAD_E_NFE: 0.0054%
- gnomAD_E_OTH: 0.0183%
- gnomAD_E_SAS: 0.0033%
- gnomAD_G_AFR: 0.0818%
- gnomAD_G_FIN: 0.0291%
- gnomAD_G_NFE: 0.0203%
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.505
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC NFE: 0.0047%
- gnomAD_E_AFR: 0.0198%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_EAS: 0.0058%
- gnomAD_E_NFE: 0.0054%
- gnomAD_E_OTH: 0.0183%
- gnomAD_E_SAS: 0.0033%
- gnomAD_G_AFR: 0.0818%
- gnomAD_G_FIN: 0.0291%
- gnomAD_G_NFE: 0.0203%
- Phenotypic similarity 0.365 to Metaphyseal anadysplasia 2 associated with MMP9.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0002979, Bowing of the legs
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0002979, Bowing of the legs
- HP:0010055, Broad hallux - HP:0002979, Bowing of the legs
- Phenotypic similarity 0.666 to mouse mutant involving MMP9.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0003072, abnormal metatarsal bone morphology
- HP:0001363, Craniosynostosis - MP:0000060, delayed bone ossification
- HP:0011304, Broad thumb - MP:0003072, abnormal metatarsal bone morphology
- HP:0010055, Broad hallux - MP:0003072, abnormal metatarsal bone morphology
- Proximity score 0.527 in interactome to RECK and phenotypic similarity 0.705 to mouse mutant of RECK.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:613073 Metaphyseal anadysplasia 2 - autosomal recessive
- ORPHA:1040 Metaphyseal anadysplasia - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.041
Phenotype Score: 0.333
Variant Score: 0.727
- Transcripts:
- MMP9:ENST00000372330.3:c.1480A>T:p.(Thr494Ser)
- Pathogenicity Data:
- Best Score: 0.727
- Polyphen2: 0.047 (B)
- SIFT: 0.273 (T)
- Frequency Data:
- No frequency data
- Proximity score 0.506 in interactome to RABL2B and phenotypic similarity 0.752 to mouse mutant of RABL2B.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis - MP:0006203, eye hemorrhage
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.040
Phenotype Score: 0.506
Variant Score: 0.529
- Pathogenicity Data:
- Best Score: 0.52900004
- SIFT: 0.471 (T)
- Frequency Data:
- TOPMed: 0.0008%
- Proximity score 0.502 in interactome to EIF3C and phenotypic similarity 1.000 to mouse mutant of EIF3C.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000562, polydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0000562, polydactyly
- HP:0010055, Broad hallux - MP:0009049, abnormal hallux morphology
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.039
Phenotype Score: 0.502
Variant Score: 0.529
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC AFR: 0.0517%
- ExAC AMR: 0.1177%
- ExAC EAS: 0.1725%
- ExAC FIN: 0.0154%
- ExAC NFE: 0.0430%
- ExAC OTH: 0.1163%
- ExAC SAS: 0.3514%
- gnomAD_G_AMR: 0.1259%
- gnomAD_G_EAS: 0.1247%
- gnomAD_G_NFE: 0.0141%
- Transcripts:
- RPL3:ENST00000216146.4:c.3+7G>C:p.?
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0998%
- TOPMed: 0.0276%
- ExAC EAS: 1.7216%
- ExAC OTH: 0.3906%
- gnomAD_E_AMR: 0.0038%
- gnomAD_E_EAS: 0.6846%
- gnomAD_E_OTH: 0.0473%
- gnomAD_G_EAS: 0.8015%
- Phenotypic similarity 0.646 to Developmental and epileptic encephalopathy 80 associated with PIGB.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001182, Tapered finger
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001199, Triphalangeal thumb
- HP:0010055, Broad hallux - HP:0001182, Tapered finger
- Proximity score 0.520 in interactome to PIGO and phenotypic similarity 0.865 to Hyperphosphatasia with mental retardation syndrome 2 associated with PIGO.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010055, Broad hallux
- HP:0001363, Craniosynostosis - HP:0011326, Anterior plagiocephaly
- HP:0011304, Broad thumb - HP:0006118, Shortening of all distal phalanges of the fingers
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:618580 Developmental and epileptic encephalopathy 80 - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.036
Phenotype Score: 0.260
Variant Score: 0.795
- Pathogenicity Data:
- Best Score: 0.795
- Polyphen2: 0.014 (B)
- SIFT: 0.205 (T)
- Frequency Data:
- TOPMed: 0.0008%
- Phenotypic similarity 0.541 to Arthrogryposis multiplex congenita 6 associated with NEB.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001181, Adducted thumb
- HP:0001363, Craniosynostosis - HP:0000239, Large fontanelles
- HP:0011304, Broad thumb - HP:0001181, Adducted thumb
- HP:0010055, Broad hallux - HP:0001181, Adducted thumb
- Phenotypic similarity 0.268 to mouse mutant involving NEB.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001344, blepharoptosis
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.504 in interactome to TNNI2 and phenotypic similarity 0.494 to Distal arthrogryposis type 1 associated with TNNI2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010557, Overlapping fingers
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001181, Adducted thumb
- HP:0010055, Broad hallux - HP:0010557, Overlapping fingers
- Proximity score 0.504 in interactome to TNNI2 and phenotypic similarity 0.611 to mouse mutant of TNNI2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0006395, abnormal epiphyseal plate morphology
- HP:0001363, Craniosynostosis - MP:0008273, abnormal intramembranous bone ossification
- HP:0011304, Broad thumb - MP:0004351, short humerus
- HP:0010055, Broad hallux - MP:0006395, abnormal epiphyseal plate morphology
- Known diseases:
- OMIM:256030 Nemaline myopathy 2, autosomal recessive - autosomal recessive
- OMIM:619334 Arthrogryposis multiplex congenita 6 - autosomal recessive
- ORPHA:171430 Severe congenital nemaline myopathy - autosomal recessive
- ORPHA:171433 Intermediate nemaline myopathy - autosomal recessive
- ORPHA:171436 Typical nemaline myopathy - autosomal recessive
- ORPHA:171439 Childhood-onset nemaline myopathy - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.035
Phenotype Score: 0.252
Variant Score: 0.800
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.028
Phenotype Score: 0.541
Variant Score: 0.447
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.541 to OMIM:619334 Arthrogryposis multiplex congenita 6
- Phenotypic similarity 0.526 to ORPHA:171430 Severe congenital nemaline myopathy
- Phenotypic similarity 0.346 to ORPHA:171436 Typical nemaline myopathy
- Phenotypic similarity 0.324 to ORPHA:171439 Childhood-onset nemaline myopathy
- Phenotypic similarity 0.237 to OMIM:256030 Nemaline myopathy 2, autosomal recessive
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.3778%
- gnomAD_G_AFR: 0.1316%
- gnomAD_G_NFE: 0.0133%
- Phenotypic similarity 0.556 to 6q25 microdeletion syndrome associated with ARID1B.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0004209, Clinodactyly of the 5th finger
- HP:0001363, Craniosynostosis - HP:0001357, Plagiocephaly
- HP:0011304, Broad thumb - HP:0100490, Camptodactyly of finger
- HP:0010055, Broad hallux - HP:0004209, Clinodactyly of the 5th finger
- Proximity score 0.507 in interactome to SMARCD2 and phenotypic similarity 0.657 to Specific granule deficiency 2 associated with SMARCD2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001156, Brachydactyly
- HP:0010055, Broad hallux - HP:0001852, Sandal gap
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:135900 Coffin-Siris syndrome 1 - autosomal dominant
- ORPHA:1465 Coffin-Siris syndrome - autosomal dominant
- ORPHA:251056 6q25 microdeletion syndrome (CNV)
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.034
Phenotype Score: 0.254
Variant Score: 0.795
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_NFE: 0.0394%
- gnomAD_G_AFR: 0.0272%
- gnomAD_G_FIN: 0.2500%
- gnomAD_G_OTH: 0.1667%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
- gnomAD_E_FIN: 0.1145%
- gnomAD_E_NFE: 0.5144%
- gnomAD_E_SAS: 0.2688%
- Proximity score 0.500 in interactome to ENPP1 and phenotypic similarity 0.697 to Autosomal recessive hypophosphatemic rickets associated with ENPP1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0002970, Genu varum
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0002982, Tibial bowing
- HP:0010055, Broad hallux - HP:0002970, Genu varum
- Proximity score 0.500 in interactome to ENPP1 and phenotypic similarity 0.578 to mouse mutant of ENPP1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0008915, fused carpal bones
- HP:0001363, Craniosynostosis - MP:0006392, abnormal nucleus pulposus morphology
- HP:0011304, Broad thumb - MP:0008915, fused carpal bones
- HP:0010055, Broad hallux - MP:0008915, fused carpal bones
- Proximity score 0.500 in interactome to ENPP1 and phenotypic similarity 0.563 to fish mutant of ENPP1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - ZP:0012007, ceratohyal cartilage premature perichondral ossification, abnormal
- HP:0011304, Broad thumb - ZP:0006782, cleithrum nodular, abnormal
- HP:0010055, Broad hallux -
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.031
Phenotype Score: 0.500
Variant Score: 0.508
- Transcripts:
- AMY2A:ENST00000414303.2:c.285A>T:p.(Arg95Ser)
- Pathogenicity Data:
- Best Score: 0.999918
- Polyphen2: 0.472 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.205 (T)
- Frequency Data:
- 1000Genomes: 0.0998%
- TOPMed: 0.0200%
- ExAC EAS: 0.4870%
- gnomAD_E_EAS: 0.4646%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_OTH: 0.0185%
- gnomAD_G_EAS: 0.2488%
- Transcripts:
- AMY2A:ENST00000414303.2:c.489C>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.500
Variant Score: 0.100
- Transcripts:
- AMY2A:ENST00000414303.2:c.489C>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.510 in interactome to FMN1 and phenotypic similarity 0.772 to mouse mutant of FMN1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.030
Phenotype Score: 0.510
Variant Score: 0.491
- Pathogenicity Data:
- Best Score: 0.999486
- Polyphen2: 0.967 (D)
- Mutation Taster: 0.999 (P)
- SIFT: 0.006 (D)
- Frequency Data:
- 1000Genomes: 0.0599%
- TOPMed: 0.0175%
- UK10K: 0.0132%
- ExAC EAS: 0.0929%
- ExAC NFE: 0.0106%
- ExAC SAS: 0.0061%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_EAS: 0.0754%
- gnomAD_E_NFE: 0.0081%
- gnomAD_E_OTH: 0.0183%
- gnomAD_E_SAS: 0.0130%
- gnomAD_G_EAS: 0.1233%
- gnomAD_G_NFE: 0.0067%
- Pathogenicity Data:
- Best Score: 0.002
- Polyphen2: 0.002 (B)
- SIFT: 1.000 (T)
- Frequency Data:
- 1000Genomes: 0.7188%
- TOPMed: 0.0654%
- ExAC AFR: 0.0096%
- ExAC EAS: 1.7102%
- ExAC NFE: 0.0015%
- ExAC SAS: 0.0484%
- gnomAD_E_AFR: 0.0131%
- gnomAD_E_EAS: 1.6872%
- gnomAD_E_NFE: 0.0045%
- gnomAD_E_OTH: 0.0911%
- gnomAD_E_SAS: 0.0487%
- gnomAD_G_EAS: 1.7901%
- Proximity score 0.507 in interactome to NLRP3 and phenotypic similarity 0.705 to CINCA syndrome associated with NLRP3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0001476, Delayed closure of the anterior fontanelle
- HP:0011304, Broad thumb - HP:0001156, Brachydactyly
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Proximity score 0.507 in interactome to NLRP3 and phenotypic similarity 0.486 to mouse mutant of NLRP3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0030825, decreased femur size
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb - MP:0030825, decreased femur size
- HP:0010055, Broad hallux - MP:0030825, decreased femur size
- Known diseases:
- OMIM:618497 Neurodevelopmental disorder with seizures and nonepileptic hyperkinetic movements - autosomal recessive
- ORPHA:442835 Non-specific early-onset epileptic encephalopathy - autosomal dominant/recessive
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.029
Phenotype Score: 0.507
Variant Score: 0.490
- Transcripts:
- CACNA1B:ENST00000277549.5:c.-2035+1_-2035+2insACGACACGGAGCCCTATTTCATCGGGATCTTTTGCTTCGAGGCAGGGATCAAAATCATCGCTCTGGGCTT:p.(=)
- CACNA1B:ENST00000277551.2:c.390+1_390+2insACGACACGGAGCCCTATTTCATCGGGATCTTTTGCTTCGAGGCAGGGATCAAAATCATCGCTCTGGGCTT:p.?
- CACNA1B:ENST00000371355.4:c.390+1_390+2insACGACACGGAGCCCTATTTCATCGGGATCTTTTGCTTCGAGGCAGGGATCAAAATCATCGCTCTGGGCTT:p.?
- CACNA1B:ENST00000371357.1:c.390+1_390+2insACGACACGGAGCCCTATTTCATCGGGATCTTTTGCTTCGAGGCAGGGATCAAAATCATCGCTCTGGGCTT:p.?
- CACNA1B:ENST00000371363.1:c.390+1_390+2insACGACACGGAGCCCTATTTCATCGGGATCTTTTGCTTCGAGGCAGGGATCAAAATCATCGCTCTGGGCTT:p.?
- CACNA1B:ENST00000371372.1:c.390+1_390+2insACGACACGGAGCCCTATTTCATCGGGATCTTTTGCTTCGAGGCAGGGATCAAAATCATCGCTCTGGGCTT:p.?
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_G_AFR: 0.6358%
- gnomAD_G_AMR: 0.6234%
- gnomAD_G_EAS: 0.5844%
- gnomAD_G_FIN: 0.3525%
- gnomAD_G_NFE: 0.4949%
- gnomAD_G_OTH: 0.3158%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0015%
- gnomAD_E_NFE: 0.0009%
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.507
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0015%
- gnomAD_E_NFE: 0.0009%
- Proximity score 0.504 in interactome to TRIP12 and phenotypic similarity 0.869 to Non-specific syndromic intellectual disability associated with TRIP12.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010109, Short hallux
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0011304, Broad thumb
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
AUTOSOMAL_DOMINANT
Exomiser Score: 0.025
Phenotype Score: 0.504
Variant Score: 0.478
- Pathogenicity Data:
- Best Score: 0.478
- SIFT: 0.522 (T)
- Frequency Data:
- gnomAD_E_NFE: 0.0009%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.009
Phenotype Score: 0.504
Variant Score: 0.370
- Pathogenicity Data:
- Best Score: 0.478
- SIFT: 0.522 (T)
- Frequency Data:
- gnomAD_E_NFE: 0.0009%
- Pathogenicity Data:
- Best Score: 0.26200002
- SIFT: 0.738 (T)
- Frequency Data:
- gnomAD_E_NFE: 0.0009%
- Proximity score 0.501 in interactome to DVL3 and phenotypic similarity 0.823 to Robinow syndrome, autosomal dominant 3 associated with DVL3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0002007, Frontal bossing
- HP:0011304, Broad thumb - HP:0011304, Broad thumb
- HP:0010055, Broad hallux - HP:0030084, Clinodactyly
- Proximity score 0.501 in interactome to DVL3 and phenotypic similarity 0.513 to mouse mutant of DVL3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0004678, split xiphoid process
- HP:0001363, Craniosynostosis - MP:0004522, abnormal orientation of cochlear hair cell stereociliary bundles
- HP:0011304, Broad thumb - MP:0004678, split xiphoid process
- HP:0010055, Broad hallux - MP:0004678, split xiphoid process
AUTOSOMAL_DOMINANT
Exomiser Score: 0.023
Phenotype Score: 0.501
Variant Score: 0.472
- Pathogenicity Data:
- Best Score: 0.473
- Polyphen2: 0.002 (B)
- SIFT: 0.527 (T)
- Frequency Data:
- ExAC NFE: 0.0097%
- gnomAD_E_NFE: 0.0024%
- gnomAD_E_SAS: 0.0039%
- Proximity score 0.500 in interactome to MDGA2 and phenotypic similarity 0.635 to mouse mutant of MDGA2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000554, abnormal carpal bone morphology
- HP:0001363, Craniosynostosis - MP:0000554, abnormal carpal bone morphology
- HP:0011304, Broad thumb - MP:0000554, abnormal carpal bone morphology
- HP:0010055, Broad hallux - MP:0000554, abnormal carpal bone morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.022
Phenotype Score: 0.500
Variant Score: 0.470
- Pathogenicity Data:
- Best Score: 0.47100002
- SIFT: 0.529 (T)
- Frequency Data:
- TOPMed: 0.0004%
- ExAC EAS: 0.0232%
- gnomAD_E_EAS: 0.0116%
- Proximity score 0.501 in interactome to PRKAR1A and phenotypic similarity 0.684 to Acrodysostosis 1, with or without hormone resistance associated with PRKAR1A.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0004490, Calvarial hyperostosis
- HP:0011304, Broad thumb - HP:0009803, Short phalanx of finger
- HP:0010055, Broad hallux - HP:0001847, Long hallux
- Proximity score 0.501 in interactome to PRKAR1A and phenotypic similarity 0.852 to mouse mutant of PRKAR1A.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002544, brachydactyly
- HP:0001363, Craniosynostosis - MP:0003419, delayed endochondral bone ossification
- HP:0011304, Broad thumb - MP:0002544, brachydactyly
- HP:0010055, Broad hallux - MP:0002544, brachydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.022
Phenotype Score: 0.501
Variant Score: 0.466
- Pathogenicity Data:
- Best Score: 0.46600002
- Polyphen2: 0.025 (B)
- SIFT: 0.534 (T)
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.272 to mouse mutant involving RAD54L.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0012121, sclerocornea
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.504 in interactome to RAD51C and phenotypic similarity 0.676 to Fanconi anemia associated with RAD51C.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001770, Toe syndactyly
- HP:0001363, Craniosynostosis - HP:0000268, Dolichocephaly
- HP:0011304, Broad thumb - HP:0001199, Triphalangeal thumb
- HP:0010055, Broad hallux - HP:0001770, Toe syndactyly
- Known diseases:
- OMIM:114480 Breast cancer, invasive ductal (susceptibility)
- OMIM:605027 Lymphoma, non-Hodgkin, somatic - unknown
AUTOSOMAL_DOMINANT
Exomiser Score: 0.019
Phenotype Score: 0.504
Variant Score: 0.446
- Pathogenicity Data:
- Best Score: 0.45
- Polyphen2: 0.001 (B)
- SIFT: 0.550 (T)
- Frequency Data:
- TOPMed: 0.0064%
- ExAC EAS: 0.0116%
- gnomAD_E_EAS: 0.0290%
- gnomAD_G_EAS: 0.0617%
- Proximity score 0.500 in interactome to SFN and phenotypic similarity 0.710 to mouse mutant of SFN.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0005306, abnormal phalanx morphology
- HP:0001363, Craniosynostosis - MP:0000454, abnormal jaw morphology
- HP:0011304, Broad thumb - MP:0005306, abnormal phalanx morphology
- HP:0010055, Broad hallux - MP:0005306, abnormal phalanx morphology
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.017
Phenotype Score: 0.500
Variant Score: 0.439
- Pathogenicity Data:
- Best Score: 0.837
- Polyphen2: 0.448 (P)
- SIFT: 0.163 (T)
- Frequency Data:
- 1000Genomes: 0.0399%
- TOPMed: 0.0399%
- ExAC AMR: 0.0259%
- ExAC EAS: 0.1040%
- ExAC NFE: 0.0105%
- gnomAD_E_AMR: 0.0119%
- gnomAD_E_EAS: 0.1045%
- gnomAD_E_NFE: 0.0107%
- gnomAD_E_OTH: 0.0365%
- gnomAD_E_SAS: 0.0097%
- gnomAD_G_AFR: 0.0114%
- gnomAD_G_EAS: 0.1233%
- gnomAD_G_NFE: 0.0200%
- gnomAD_G_OTH: 0.1022%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC AFR: 0.0288%
- ExAC AMR: 0.0432%
- ExAC EAS: 0.0925%
- ExAC NFE: 0.0030%
- ExAC OTH: 0.1109%
- ExAC SAS: 1.4514%
- gnomAD_E_AFR: 0.0327%
- gnomAD_E_AMR: 0.0238%
- gnomAD_E_EAS: 0.0812%
- gnomAD_E_NFE: 0.0036%
- gnomAD_E_OTH: 0.0365%
- gnomAD_E_SAS: 1.3941%
- gnomAD_G_AFR: 0.0459%
- gnomAD_G_EAS: 0.0621%
- Proximity score 0.502 in interactome to PSEN1 and phenotypic similarity 0.175 to Familial isolated dilated cardiomyopathy associated with PSEN1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0000982, Palmoplantar keratoderma
- HP:0010055, Broad hallux - HP:0000982, Palmoplantar keratoderma
- Proximity score 0.502 in interactome to PSEN1 and phenotypic similarity 0.685 to mouse mutant of PSEN1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000592, short tail
- HP:0001363, Craniosynostosis - MP:0003843, abnormal sagittal suture morphology
- HP:0011304, Broad thumb - MP:0000592, short tail
- HP:0010055, Broad hallux - MP:0000592, short tail
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.502
Variant Score: 0.433
- Transcripts:
- ERN1:ENST00000433197.3:c.1279G>A:p.(Ala427Thr)
- Pathogenicity Data:
- Best Score: 0.43699998
- Polyphen2: 0.002 (B)
- SIFT: 0.563 (T)
- Frequency Data:
- TOPMed: 0.0060%
- ESP AA: 0.0250%
- ESP All: 0.0081%
- ExAC FIN: 0.0414%
- ExAC NFE: 0.0160%
- ExAC SAS: 0.0079%
- gnomAD_E_AMR: 0.0031%
- gnomAD_E_EAS: 0.0060%
- gnomAD_E_FIN: 0.0366%
- gnomAD_E_NFE: 0.0102%
- gnomAD_G_EAS: 0.0617%
- gnomAD_G_FIN: 0.0287%
- gnomAD_G_NFE: 0.0133%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.996 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.014
Phenotype Score: 0.000
Variant Score: 0.985
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.996 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.972
- Polyphen2: 0.010 (B)
- SIFT: 0.028 (D)
- Frequency Data:
- UK10K: 0.0132%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_SAS: 0.0195%
- gnomAD_G_AFR: 0.0122%
- gnomAD_G_NFE: 0.0135%
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.944 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- gnomAD_G_AFR: 0.1652%
- gnomAD_G_EAS: 0.2146%
- gnomAD_G_NFE: 0.0068%
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.471 (P)
- Mutation Taster: 1.000 (P)
- SIFT: 0.028 (D)
- Frequency Data:
- 1000Genomes: 0.1797%
- TOPMed: 0.1797%
- gnomAD_E_NFE: 0.0009%
- gnomAD_G_AFR: 0.1322%
- gnomAD_G_EAS: 0.2941%
- gnomAD_G_NFE: 0.0137%
- Pathogenicity Data:
- Best Score: 0.612
- Polyphen2: 0.013 (B)
- SIFT: 0.388 (T)
- Frequency Data:
- UK10K: 0.0132%
- gnomAD_E_AFR: 0.0066%
- gnomAD_E_AMR: 0.0298%
- gnomAD_E_EAS: 0.0058%
- gnomAD_E_FIN: 0.0179%
- gnomAD_E_NFE: 0.0673%
- gnomAD_E_OTH: 0.0548%
- gnomAD_E_SAS: 0.0033%
- Pathogenicity Data:
- Best Score: 0.993
- Polyphen2: 0.006 (B)
- SIFT: 0.007 (D)
- Frequency Data:
- gnomAD_E_AFR: 0.0066%
- gnomAD_E_AMR: 0.0328%
- gnomAD_E_NFE: 0.0018%
- gnomAD_E_OTH: 0.0548%
- gnomAD_E_SAS: 0.0032%
- gnomAD_G_AFR: 1.7907%
- gnomAD_G_AMR: 0.1302%
- gnomAD_G_EAS: 1.5228%
- gnomAD_G_FIN: 0.1180%
- gnomAD_G_NFE: 0.0560%
- gnomAD_G_OTH: 0.1087%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0197%
- gnomAD_E_NFE: 0.0018%
- gnomAD_E_SAS: 0.0032%
- gnomAD_G_AFR: 0.0471%
- gnomAD_G_NFE: 0.0067%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_G_AFR: 0.0125%
- gnomAD_G_EAS: 0.0668%
- gnomAD_G_NFE: 0.0069%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_G_EAS: 0.0678%
- gnomAD_G_NFE: 0.0069%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_G_AFR: 0.0629%
- gnomAD_G_EAS: 0.1376%
- gnomAD_G_NFE: 0.0068%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0998%
- TOPMed: 0.0998%
- gnomAD_E_AFR: 0.1244%
- gnomAD_E_AMR: 0.0089%
- gnomAD_E_NFE: 0.0063%
- gnomAD_E_OTH: 0.0183%
- gnomAD_E_SAS: 0.0976%
- gnomAD_G_AFR: 0.1686%
- gnomAD_G_NFE: 0.0136%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_G_AFR: 0.1812%
- gnomAD_G_EAS: 0.2152%
- gnomAD_G_NFE: 0.0136%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC AFR: 0.0204%
- ExAC EAS: 0.0116%
- ExAC NFE: 0.0015%
- ExAC SAS: 0.0303%
- gnomAD_E_AFR: 0.0131%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_SAS: 0.0227%
- gnomAD_G_AFR: 0.2503%
- gnomAD_G_EAS: 0.2915%
- gnomAD_G_NFE: 0.0137%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0066%
- gnomAD_E_SAS: 0.0033%
- gnomAD_G_AFR: 0.3233%
- gnomAD_G_EAS: 0.6192%
- gnomAD_G_NFE: 0.0141%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0799%
- TOPMed: 0.0234%
- ExAC EAS: 0.6378%
- ExAC NFE: 0.0015%
- ExAC SAS: 0.0122%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_EAS: 0.5532%
- gnomAD_E_NFE: 0.0019%
- gnomAD_E_OTH: 0.0191%
- gnomAD_E_SAS: 0.0101%
- gnomAD_G_EAS: 0.8301%
- gnomAD_G_NFE: 0.0085%
- Pathogenicity Data:
- Best Score: 0.184
- Polyphen2: 0.184 (B)
- SIFT: 1.000 (T)
- Frequency Data:
- 1000Genomes: 0.3195%
- TOPMed: 0.3195%
- ExAC AFR: 0.0434%
- ExAC AMR: 0.2236%
- ExAC EAS: 1.7005%
- ExAC NFE: 0.0830%
- ExAC OTH: 1.0938%
- ExAC SAS: 0.7985%
- gnomAD_E_AFR: 0.0274%
- gnomAD_E_AMR: 0.0547%
- gnomAD_E_EAS: 0.0484%
- gnomAD_E_NFE: 0.0014%
- gnomAD_E_SAS: 0.0633%
- gnomAD_G_AFR: 0.0273%
- gnomAD_G_AMR: 0.3390%
- gnomAD_G_EAS: 0.5785%
- gnomAD_G_NFE: 0.1383%
- gnomAD_G_OTH: 0.1639%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 1.0780%
- TOPMed: 1.0780%
- gnomAD_E_AFR: 0.2453%
- gnomAD_E_AMR: 0.0193%
- gnomAD_E_NFE: 0.0024%
- gnomAD_E_OTH: 0.0230%
- gnomAD_E_SAS: 0.0083%
- gnomAD_G_AFR: 1.1684%
- gnomAD_G_AMR: 0.1404%
- gnomAD_G_EAS: 0.3981%
- gnomAD_G_NFE: 0.1363%
- gnomAD_G_OTH: 0.5348%
- No phenotype or PPI evidence
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0200%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0066%
- gnomAD_E_AMR: 0.0543%
- gnomAD_E_EAS: 0.0060%
- gnomAD_E_FIN: 0.0046%
- gnomAD_E_NFE: 0.0252%
- gnomAD_E_OTH: 0.0190%
- gnomAD_E_SAS: 0.0803%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0515%
- gnomAD_E_AMR: 0.0341%
- gnomAD_E_EAS: 0.0198%
- gnomAD_E_FIN: 0.0228%
- gnomAD_E_NFE: 0.0573%
- gnomAD_E_OTH: 0.0287%
- gnomAD_E_SAS: 0.0467%
- gnomAD_G_AFR: 0.0910%
- gnomAD_G_EAS: 0.1253%
- gnomAD_G_NFE: 0.0515%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC AFR: 0.1137%
- ExAC AMR: 0.0087%
- ExAC EAS: 0.2110%
- ExAC FIN: 0.0152%
- ExAC NFE: 0.0153%
- ExAC SAS: 0.0061%
- gnomAD_E_AFR: 0.0268%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_EAS: 0.1000%
- gnomAD_E_NFE: 0.0063%
- gnomAD_E_OTH: 0.0184%
- gnomAD_E_SAS: 0.0066%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0070%
- gnomAD_E_AMR: 0.0385%
- gnomAD_E_EAS: 0.2344%
- gnomAD_E_NFE: 0.0199%
- gnomAD_E_OTH: 0.0195%
- gnomAD_E_SAS: 0.0105%
- gnomAD_G_AFR: 0.0116%
- gnomAD_G_EAS: 0.0708%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.986 (D)
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.979 (D)
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.998
- Polyphen2: 0.998 (D)
- SIFT: 0.003 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.996
- Polyphen2: 0.888 (P)
- SIFT: 0.004 (D)
- Frequency Data:
- TOPMed: 0.0004%
- Pathogenicity Data:
- Best Score: 0.993
- Polyphen2: 0.944 (P)
- SIFT: 0.007 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.993
- Polyphen2: 0.971 (D)
- SIFT: 0.007 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.99
- Polyphen2: 0.101 (B)
- SIFT: 0.010 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.986
- Polyphen2: 0.986 (D)
- SIFT: 0.016 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.982
- Polyphen2: 0.982 (D)
- SIFT: 0.050 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.979
- Polyphen2: 0.246 (B)
- SIFT: 0.021 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.964
- Polyphen2: 0.001 (B)
- SIFT: 0.036 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.959
- Polyphen2: 0.002 (B)
- SIFT: 0.041 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.943
- Polyphen2: 0.943 (P)
- SIFT: 0.076 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.94200003
- Polyphen2: 0.905 (P)
- SIFT: 0.058 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.939
- Polyphen2: 0.001 (B)
- SIFT: 0.061 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.889
- Polyphen2: 0.001 (B)
- SIFT: 0.111 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.833
- Polyphen2: 0.015 (B)
- SIFT: 0.167 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.815
- Polyphen2: 0.001 (B)
- SIFT: 0.185 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.758
- Polyphen2: 0.181 (B)
- SIFT: 0.242 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.652
- Polyphen2: 0.003 (B)
- SIFT: 0.348 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.599
- SIFT: 0.401 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.376
- Polyphen2: 0.001 (B)
- SIFT: 0.624 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.112999976
- SIFT: 0.887 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.008000016
- SIFT: 0.992 (T)
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Transcripts:
- HLA-DRB6:ENST00000411500.1:n.852-2A>G:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.007
Phenotype Score: 0.000
Variant Score: 0.900
- Transcripts:
- HLA-DRB6:ENST00000411500.1:n.852-2A>G:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- HLA-DRB6:ENST00000411500.1:n.852-3C>T:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- HLA-DRB6:ENST00000411500.1:n.852-7T>C:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Transcripts:
- KIR2DL4:ENST00000345540.5:c.484_485del:p.(Glu162Serfs*3)
- KIR2DL4:ENST00000346587.4:c.199_200del:p.(Glu67Serfs*3)
- KIR2DL4:ENST00000357494.4:c.484_485del:p.(Glu162Serfs*3)
- KIR2DL4:ENST00000359085.4:c.484_485del:p.(Glu162Serfs*3)
- KIR2DL4:ENST00000396284.2:c.478_479del:p.(Glu160Serfs*3)
- KIR2DL4:ENST00000396293.1:c.199_200del:p.(Glu67Serfs*3)
- KIR2DL4:ENST00000402254.2:c.35-11461_35-11460del:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-11461_35-11460del:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-11461_35-11460del:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Transcripts:
- KIR2DL4:ENST00000345540.5:c.484_485del:p.(Glu162Serfs*3)
- KIR2DL4:ENST00000346587.4:c.199_200del:p.(Glu67Serfs*3)
- KIR2DL4:ENST00000357494.4:c.484_485del:p.(Glu162Serfs*3)
- KIR2DL4:ENST00000359085.4:c.484_485del:p.(Glu162Serfs*3)
- KIR2DL4:ENST00000396284.2:c.478_479del:p.(Glu160Serfs*3)
- KIR2DL4:ENST00000396293.1:c.199_200del:p.(Glu67Serfs*3)
- KIR2DL4:ENST00000402254.2:c.35-11461_35-11460del:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-11461_35-11460del:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-11461_35-11460del:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL4:ENST00000345540.5:c.487_488insGG:p.(Ala163Glyfs*78)
- KIR2DL4:ENST00000357494.4:c.487_488insGG:p.(Ala163Glyfs*61)
- KIR2DL4:ENST00000396293.1:c.202_203insGG:p.(Ala68Glyfs*61)
- KIR2DL4:ENST00000346587.4:c.202_203insGG:p.(Ala68Glyfs*78)
- KIR2DL4:ENST00000359085.4:c.487_488insGG:p.(Ala163Glyfs*83)
- KIR2DL4:ENST00000396284.2:c.481_482insGG:p.(Ala161Glyfs*83)
- KIR2DL4:ENST00000402254.2:c.35-11459_35-11458insGG:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-11459_35-11458insGG:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-11459_35-11458insGG:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL4:ENST00000345540.5:c.674_675del:p.(Trp225Serfs*5)
- KIR2DL4:ENST00000346587.4:c.389_390del:p.(Trp130Serfs*5)
- KIR2DL4:ENST00000359085.4:c.674_675del:p.(Trp225Serfs*5)
- KIR2DL4:ENST00000396284.2:c.668_669del:p.(Trp223Serfs*5)
- KIR2DL4:ENST00000402254.2:c.35-8683_35-8682del:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-8683_35-8682del:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-8683_35-8682del:p.(=)
- KIR2DL4:ENST00000357494.4:c.655+2607_655+2608del:p.(=)
- KIR2DL4:ENST00000396293.1:c.370+2607_370+2608del:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL4:ENST00000345540.5:c.676_677insAT:p.(Pro226Hisfs*15)
- KIR2DL4:ENST00000346587.4:c.391_392insAT:p.(Pro131Hisfs*15)
- KIR2DL4:ENST00000359085.4:c.676_677insAT:p.(Pro226Hisfs*20)
- KIR2DL4:ENST00000396284.2:c.670_671insAT:p.(Pro224Hisfs*20)
- KIR2DL4:ENST00000402254.2:c.35-8681_35-8680insAT:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-8681_35-8680insAT:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-8681_35-8680insAT:p.(=)
- KIR2DL4:ENST00000357494.4:c.655+2609_655+2610insAT:p.(=)
- KIR2DL4:ENST00000396293.1:c.370+2609_370+2610insAT:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL4:ENST00000359085.4:c.811dup:p.(Met271Asnfs*108)
- KIR2DL4:ENST00000396284.2:c.804dup:p.(Val269Serfs*43)
- KIR2DL4:ENST00000402254.2:c.35-4315_35-4314insA:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-4315_35-4314insA:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-4315_35-4314insA:p.(=)
- KIR2DL4:ENST00000345540.5:c.707-471_707-470insA:p.(=)
- KIR2DL4:ENST00000346587.4:c.422-471_422-470insA:p.(=)
- KIR2DL4:ENST00000357494.4:c.656-471_656-470insA:p.(=)
- KIR2DL4:ENST00000396293.1:c.371-471_371-470insA:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL4:ENST00000345540.5:c.445C>A:p.(Gln149Lys)
- KIR2DL4:ENST00000346587.4:c.160C>A:p.(Gln54Lys)
- KIR2DL4:ENST00000357494.4:c.445C>A:p.(Gln149Lys)
- KIR2DL4:ENST00000359085.4:c.445C>A:p.(Gln149Lys)
- KIR2DL4:ENST00000396284.2:c.439C>A:p.(Gln147Lys)
- KIR2DL4:ENST00000396293.1:c.160C>A:p.(Gln54Lys)
- KIR2DL4:ENST00000402254.2:c.35-11500C>A:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-11500C>A:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-11500C>A:p.(=)
- Pathogenicity Data:
- Best Score: 0.985
- Polyphen2: 0.060 (B)
- SIFT: 0.015 (D)
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL4:ENST00000345540.5:c.368A>T:p.(Tyr123Phe)
- KIR2DL4:ENST00000346587.4:c.83A>T:p.(Tyr28Phe)
- KIR2DL4:ENST00000357494.4:c.368A>T:p.(Tyr123Phe)
- KIR2DL4:ENST00000359085.4:c.368A>T:p.(Tyr123Phe)
- KIR2DL4:ENST00000396284.2:c.362A>T:p.(Tyr121Phe)
- KIR2DL4:ENST00000396293.1:c.83A>T:p.(Tyr28Phe)
- KIR2DL4:ENST00000402254.2:c.35-11577A>T:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-11577A>T:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-11577A>T:p.(=)
- Pathogenicity Data:
- Best Score: 0.917
- Polyphen2: 0.168 (B)
- SIFT: 0.083 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL4:ENST00000345540.5:c.497T>C:p.(Leu166Pro)
- KIR2DL4:ENST00000346587.4:c.212T>C:p.(Leu71Pro)
- KIR2DL4:ENST00000357494.4:c.497T>C:p.(Leu166Pro)
- KIR2DL4:ENST00000359085.4:c.497T>C:p.(Leu166Pro)
- KIR2DL4:ENST00000396284.2:c.491T>C:p.(Leu164Pro)
- KIR2DL4:ENST00000396293.1:c.212T>C:p.(Leu71Pro)
- KIR2DL4:ENST00000402254.2:c.35-11448T>C:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-11448T>C:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-11448T>C:p.(=)
- Pathogenicity Data:
- Best Score: 0.887
- Polyphen2: 0.012 (B)
- SIFT: 0.113 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL4:ENST00000345540.5:c.371A>G:p.(Glu124Gly)
- KIR2DL4:ENST00000346587.4:c.86A>G:p.(Glu29Gly)
- KIR2DL4:ENST00000357494.4:c.371A>G:p.(Glu124Gly)
- KIR2DL4:ENST00000359085.4:c.371A>G:p.(Glu124Gly)
- KIR2DL4:ENST00000396284.2:c.365A>G:p.(Glu122Gly)
- KIR2DL4:ENST00000396293.1:c.86A>G:p.(Glu29Gly)
- KIR2DL4:ENST00000402254.2:c.35-11574A>G:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-11574A>G:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-11574A>G:p.(=)
- Pathogenicity Data:
- Best Score: 0.878
- Polyphen2: 0.006 (B)
- SIFT: 0.122 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL4:ENST00000345540.5:c.661C>T:p.(Pro221Ser)
- KIR2DL4:ENST00000346587.4:c.376C>T:p.(Pro126Ser)
- KIR2DL4:ENST00000359085.4:c.661C>T:p.(Pro221Ser)
- KIR2DL4:ENST00000396284.2:c.655C>T:p.(Pro219Ser)
- KIR2DL4:ENST00000402254.2:c.35-8696C>T:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-8696C>T:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-8696C>T:p.(=)
- KIR2DL4:ENST00000357494.4:c.655+2594C>T:p.(=)
- KIR2DL4:ENST00000396293.1:c.370+2594C>T:p.(=)
- Pathogenicity Data:
- Best Score: 0.82
- Polyphen2: 0.003 (B)
- SIFT: 0.180 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL4:ENST00000345540.5:c.706+3A>G:p.?
- KIR2DL4:ENST00000346587.4:c.421+3A>G:p.?
- KIR2DL4:ENST00000359085.4:c.706+3A>G:p.?
- KIR2DL4:ENST00000396284.2:c.700+3A>G:p.?
- KIR2DL4:ENST00000402254.2:c.35-8648A>G:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-8648A>G:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-8648A>G:p.(=)
- KIR2DL4:ENST00000357494.4:c.655+2642A>G:p.(=)
- KIR2DL4:ENST00000396293.1:c.370+2642A>G:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL4:ENST00000345540.5:c.706+7del:p.?
- KIR2DL4:ENST00000346587.4:c.421+7del:p.?
- KIR2DL4:ENST00000359085.4:c.706+7del:p.?
- KIR2DL4:ENST00000396284.2:c.700+7del:p.?
- KIR2DL4:ENST00000402254.2:c.35-8644del:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-8644del:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-8644del:p.(=)
- KIR2DL4:ENST00000357494.4:c.655+2646del:p.(=)
- KIR2DL4:ENST00000396293.1:c.370+2646del:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL4:ENST00000345540.5:c.385A>T:p.(Thr129Ser)
- KIR2DL4:ENST00000346587.4:c.100A>T:p.(Thr34Ser)
- KIR2DL4:ENST00000357494.4:c.385A>T:p.(Thr129Ser)
- KIR2DL4:ENST00000359085.4:c.385A>T:p.(Thr129Ser)
- KIR2DL4:ENST00000396284.2:c.379A>T:p.(Thr127Ser)
- KIR2DL4:ENST00000396293.1:c.100A>T:p.(Thr34Ser)
- KIR2DL4:ENST00000402254.2:c.35-11560A>T:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-11560A>T:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-11560A>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL4:ENST00000345540.5:c.384T>C:p.(=)
- KIR2DL4:ENST00000346587.4:c.99T>C:p.(=)
- KIR2DL4:ENST00000357494.4:c.384T>C:p.(=)
- KIR2DL4:ENST00000359085.4:c.384T>C:p.(=)
- KIR2DL4:ENST00000396284.2:c.378T>C:p.(=)
- KIR2DL4:ENST00000396293.1:c.99T>C:p.(=)
- KIR2DL4:ENST00000402254.2:c.35-11561T>C:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-11561T>C:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-11561T>C:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL4:ENST00000345540.5:c.453C>A:p.(=)
- KIR2DL4:ENST00000346587.4:c.168C>A:p.(=)
- KIR2DL4:ENST00000357494.4:c.453C>A:p.(=)
- KIR2DL4:ENST00000359085.4:c.453C>A:p.(=)
- KIR2DL4:ENST00000396284.2:c.447C>A:p.(=)
- KIR2DL4:ENST00000396293.1:c.168C>A:p.(=)
- KIR2DL4:ENST00000402254.2:c.35-11492C>A:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-11492C>A:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-11492C>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL4:ENST00000345540.5:c.540C>T:p.(=)
- KIR2DL4:ENST00000346587.4:c.255C>T:p.(=)
- KIR2DL4:ENST00000357494.4:c.540C>T:p.(=)
- KIR2DL4:ENST00000359085.4:c.540C>T:p.(=)
- KIR2DL4:ENST00000396284.2:c.534C>T:p.(=)
- KIR2DL4:ENST00000396293.1:c.255C>T:p.(=)
- KIR2DL4:ENST00000402254.2:c.35-11405C>T:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-11405C>T:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-11405C>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL4:ENST00000345540.5:c.666T>A:p.(=)
- KIR2DL4:ENST00000346587.4:c.381T>A:p.(=)
- KIR2DL4:ENST00000359085.4:c.666T>A:p.(=)
- KIR2DL4:ENST00000396284.2:c.660T>A:p.(=)
- KIR2DL4:ENST00000402254.2:c.35-8691T>A:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-8691T>A:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-8691T>A:p.(=)
- KIR2DL4:ENST00000357494.4:c.655+2599T>A:p.(=)
- KIR2DL4:ENST00000396293.1:c.370+2599T>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL4:ENST00000345540.5:c.381G>A:p.(=)
- KIR2DL4:ENST00000346587.4:c.96G>A:p.(=)
- KIR2DL4:ENST00000357494.4:c.381G>A:p.(=)
- KIR2DL4:ENST00000359085.4:c.381G>A:p.(=)
- KIR2DL4:ENST00000396284.2:c.375G>A:p.(=)
- KIR2DL4:ENST00000396293.1:c.96G>A:p.(=)
- KIR2DL4:ENST00000402254.2:c.35-11564G>A:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-11564G>A:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-11564G>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC AMR: 0.0693%
- ExAC NFE: 0.0895%
- gnomAD_E_AMR: 0.0204%
- gnomAD_E_NFE: 0.0097%
- gnomAD_G_NFE: 0.0217%
- Transcripts:
- KIR2DL4:ENST00000345540.5:c.462C>G:p.(Ile154Met)
- KIR2DL4:ENST00000346587.4:c.177C>G:p.(Ile59Met)
- KIR2DL4:ENST00000357494.4:c.462C>G:p.(Ile154Met)
- KIR2DL4:ENST00000359085.4:c.462C>G:p.(Ile154Met)
- KIR2DL4:ENST00000396284.2:c.456C>G:p.(Ile152Met)
- KIR2DL4:ENST00000396293.1:c.177C>G:p.(Ile59Met)
- KIR2DL4:ENST00000402254.2:c.35-11483C>G:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-11483C>G:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-11483C>G:p.(=)
- Pathogenicity Data:
- Best Score: 0.06
- Polyphen2: 0.060 (B)
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL4:ENST00000345540.5:c.446A>G:p.(Gln149Arg)
- KIR2DL4:ENST00000346587.4:c.161A>G:p.(Gln54Arg)
- KIR2DL4:ENST00000357494.4:c.446A>G:p.(Gln149Arg)
- KIR2DL4:ENST00000359085.4:c.446A>G:p.(Gln149Arg)
- KIR2DL4:ENST00000396284.2:c.440A>G:p.(Gln147Arg)
- KIR2DL4:ENST00000396293.1:c.161A>G:p.(Gln54Arg)
- KIR2DL4:ENST00000402254.2:c.35-11499A>G:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-11499A>G:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-11499A>G:p.(=)
- Pathogenicity Data:
- Best Score: 0.02
- Polyphen2: 0.020 (B)
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL4:ENST00000345540.5:c.698T>C:p.(Phe233Ser)
- KIR2DL4:ENST00000346587.4:c.413T>C:p.(Phe138Ser)
- KIR2DL4:ENST00000359085.4:c.698T>C:p.(Phe233Ser)
- KIR2DL4:ENST00000396284.2:c.692T>C:p.(Phe231Ser)
- KIR2DL4:ENST00000402254.2:c.35-8659T>C:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-8659T>C:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-8659T>C:p.(=)
- KIR2DL4:ENST00000357494.4:c.655+2631T>C:p.(=)
- KIR2DL4:ENST00000396293.1:c.370+2631T>C:p.(=)
- Pathogenicity Data:
- Best Score: 0.002
- Polyphen2: 0.002 (B)
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL4:ENST00000345540.5:c.520A>G:p.(Ile174Val)
- KIR2DL4:ENST00000346587.4:c.235A>G:p.(Ile79Val)
- KIR2DL4:ENST00000357494.4:c.520A>G:p.(Ile174Val)
- KIR2DL4:ENST00000359085.4:c.520A>G:p.(Ile174Val)
- KIR2DL4:ENST00000396284.2:c.514A>G:p.(Ile172Val)
- KIR2DL4:ENST00000396293.1:c.235A>G:p.(Ile79Val)
- KIR2DL4:ENST00000402254.2:c.35-11425A>G:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-11425A>G:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-11425A>G:p.(=)
- Pathogenicity Data:
- Best Score: 0.001
- Polyphen2: 0.001 (B)
- Frequency Data:
- No frequency data
- Transcripts:
- KIR2DL4:ENST00000345540.5:c.392G>A:p.(Arg131Gln)
- KIR2DL4:ENST00000346587.4:c.107G>A:p.(Arg36Gln)
- KIR2DL4:ENST00000357494.4:c.392G>A:p.(Arg131Gln)
- KIR2DL4:ENST00000359085.4:c.392G>A:p.(Arg131Gln)
- KIR2DL4:ENST00000396284.2:c.386G>A:p.(Arg129Gln)
- KIR2DL4:ENST00000396293.1:c.107G>A:p.(Arg36Gln)
- KIR2DL4:ENST00000402254.2:c.35-11553G>A:p.(=)
- KIR2DL4:ENST00000538269.1:c.35-11553G>A:p.(=)
- KIR2DL4:ENST00000541392.1:c.35-11553G>A:p.(=)
- Pathogenicity Data:
- Best Score: 0.001
- Polyphen2: 0.001 (B)
- Frequency Data:
- gnomAD_E_AMR: 0.0235%
- gnomAD_E_NFE: 0.0071%
- gnomAD_E_SAS: 0.0596%
- gnomAD_G_AFR: 0.0379%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_EAS: 0.0122%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 1.5180%
- TOPMed: 1.5180%
- ExAC AFR: 0.0098%
- ExAC EAS: 0.0120%
- gnomAD_E_EAS: 0.0181%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 1.5180%
- TOPMed: 1.5180%
- ExAC EAS: 0.0120%
- gnomAD_E_EAS: 0.0182%
- gnomAD_E_NFE: 0.0019%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 1.9570%
- TOPMed: 1.9570%
- ExAC AFR: 0.0784%
- ExAC AMR: 0.0366%
- ExAC EAS: 0.0361%
- ExAC FIN: 0.1796%
- ExAC NFE: 0.1766%
- ExAC OTH: 0.3529%
- ExAC SAS: 0.0832%
- gnomAD_E_AFR: 0.0133%
- gnomAD_E_AMR: 0.0160%
- gnomAD_E_EAS: 0.0182%
- gnomAD_E_FIN: 0.0578%
- gnomAD_E_NFE: 0.0972%
- gnomAD_E_OTH: 0.0195%
- gnomAD_E_SAS: 0.0297%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Transcripts:
- MUC19:ENST00000454784.4:c.3884-1_3884insACCAG:p.?
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Transcripts:
- RAD17:ENST00000282891.6:c.208C>T:p.(Pro70Ser)
- RAD17:ENST00000305138.4:c.466C>T:p.(Pro156Ser)
- RAD17:ENST00000345306.6:c.466C>T:p.(Pro156Ser)
- RAD17:ENST00000354312.3:c.466C>T:p.(Pro156Ser)
- RAD17:ENST00000354868.5:c.466C>T:p.(Pro156Ser)
- RAD17:ENST00000361732.2:c.466C>T:p.(Pro156Ser)
- RAD17:ENST00000380774.3:c.499C>T:p.(Pro167Ser)
- RAD17:ENST00000509734.1:c.499C>T:p.(Pro167Ser)
- RAD17:ENST00000358030.2:c.-30C>T:p.(=)
- RAD17:ENST00000521422.1:c.-30C>T:p.(=)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.003 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.176 (T)
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.007
Phenotype Score: 0.000
Variant Score: 0.900
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.002 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.076 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 1.000 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.001 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.135 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.014 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.056 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.020 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.002 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.005 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.006 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.002 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.003 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.005 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.029 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.023 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.021 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.002 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- SIFT: 0.000 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.999999
- Mutation Taster: 1.000 (P)
- SIFT: 1.000 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.027 (D)
- Frequency Data:
- gnomAD_E_NFE: 0.0020%
- Pathogenicity Data:
- Best Score: 0.999
- SIFT: 0.001 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.999
- Mutation Taster: 0.864
- SIFT: 0.001 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
- gnomAD_E_NFE: 0.0092%
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.080 (T)
- Frequency Data:
- gnomAD_E_EAS: 0.0116%
- Pathogenicity Data:
- Best Score: 0.998
- SIFT: 0.002 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- gnomAD_E_AFR: 0.0290%
- Pathogenicity Data:
- Best Score: 0.999999
- Mutation Taster: 1.000 (P)
- SIFT: 0.084 (T)
- Frequency Data:
- 1000Genomes: 0.0399%
- TOPMed: 0.0399%
- gnomAD_E_AFR: 0.0152%
- gnomAD_E_EAS: 0.0111%
- gnomAD_E_OTH: 0.0275%
- gnomAD_G_AFR: 0.0132%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AMR: 0.0146%
- gnomAD_E_NFE: 0.0163%
- gnomAD_E_SAS: 0.0551%
- gnomAD_G_AFR: 0.0185%
- gnomAD_G_NFE: 0.0094%
- Pathogenicity Data:
- Best Score: 0.992
- SIFT: 0.008 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.031 (D)
- Frequency Data:
- gnomAD_E_EAS: 0.0676%
- Pathogenicity Data:
- Best Score: 0.987
- SIFT: 0.013 (D)
- Frequency Data:
- gnomAD_E_NFE: 0.0058%
- Pathogenicity Data:
- Best Score: 0.982
- SIFT: 0.018 (D)
- Frequency Data:
- TOPMed: 0.0004%
- Pathogenicity Data:
- Best Score: 0.978051
- Mutation Taster: 0.978 (P)
- SIFT: 0.124 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- ZNF717:ENST00000477374.1:c.278G>T:p.(Gly93Val)
- Pathogenicity Data:
- Best Score: 0.978
- SIFT: 0.022 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.977
- SIFT: 0.023 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.973
- SIFT: 0.027 (D)
- Frequency Data:
- No frequency data
- Transcripts:
- ZNF717:ENST00000477374.1:c.293A>C:p.(Gln98Pro)
- Pathogenicity Data:
- Best Score: 0.969
- SIFT: 0.031 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.962
- SIFT: 0.038 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.951
- SIFT: 0.049 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.939
- SIFT: 0.061 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.93299997
- SIFT: 0.067 (T)
- Frequency Data:
- gnomAD_E_AMR: 0.0215%
- gnomAD_E_NFE: 0.0018%
- gnomAD_E_OTH: 0.0270%
- gnomAD_E_SAS: 0.0198%
- gnomAD_G_AFR: 0.0135%
- gnomAD_G_NFE: 0.0148%
- Pathogenicity Data:
- Best Score: 0.928
- SIFT: 0.072 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.901
- SIFT: 0.099 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.902
- SIFT: 0.098 (T)
- Frequency Data:
- gnomAD_E_EAS: 0.0148%
- Pathogenicity Data:
- Best Score: 0.898
- SIFT: 0.102 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.879
- SIFT: 0.121 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.878
- SIFT: 0.122 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.943
- SIFT: 0.057 (D)
- Frequency Data:
- gnomAD_E_AFR: 0.0215%
- gnomAD_E_NFE: 0.0271%
- gnomAD_E_SAS: 0.4466%
- gnomAD_G_AFR: 0.0223%
- gnomAD_G_NFE: 0.0231%
- Pathogenicity Data:
- Best Score: 0.86800003
- SIFT: 0.132 (T)
- Frequency Data:
- gnomAD_E_AFR: 0.0313%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.837
- SIFT: 0.163 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.806
- SIFT: 0.194 (T)
- Frequency Data:
- gnomAD_E_SAS: 0.0159%
- Pathogenicity Data:
- Best Score: 0.803
- SIFT: 0.197 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.796
- SIFT: 0.204 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.786
- SIFT: 0.214 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.763
- SIFT: 0.237 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.741
- SIFT: 0.259 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.726
- SIFT: 0.274 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.713
- SIFT: 0.287 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.7
- SIFT: 0.300 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.68200004
- SIFT: 0.318 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.671
- SIFT: 0.329 (T)
- Frequency Data:
- TOPMed: 0.0038%
- Pathogenicity Data:
- Best Score: 0.649
- SIFT: 0.351 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.62
- SIFT: 0.380 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.616
- SIFT: 0.384 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.62
- SIFT: 0.380 (T)
- Frequency Data:
- gnomAD_G_AFR: 0.0804%
- Pathogenicity Data:
- Best Score: 0.60899997
- SIFT: 0.391 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.595
- SIFT: 0.405 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.593
- SIFT: 0.407 (T)
- Frequency Data:
- gnomAD_E_NFE: 0.0091%
- gnomAD_G_AMR: 0.4785%
- gnomAD_G_EAS: 0.2252%
- gnomAD_G_FIN: 0.4098%
- gnomAD_G_NFE: 0.0948%
- gnomAD_G_OTH: 0.4608%
- Transcripts:
- ZNF717:ENST00000477374.1:c.307A>G:p.(Ile103Val)
- Pathogenicity Data:
- Best Score: 0.538
- SIFT: 0.462 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.525
- SIFT: 0.475 (T)
- Frequency Data:
- gnomAD_E_NFE: 0.0039%
- Pathogenicity Data:
- Best Score: 0.513
- SIFT: 0.487 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.513
- SIFT: 0.487 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.50699997
- SIFT: 0.493 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.49400002
- SIFT: 0.506 (T)
- Frequency Data:
- TOPMed: 0.0008%
- Pathogenicity Data:
- Best Score: 0.621
- SIFT: 0.379 (T)
- Frequency Data:
- ExAC AFR: 0.3497%
- ExAC NFE: 0.2069%
- ExAC SAS: 0.0965%
- gnomAD_E_AFR: 0.4339%
- gnomAD_E_AMR: 1.0563%
- gnomAD_E_EAS: 0.6369%
- gnomAD_E_FIN: 0.0977%
- gnomAD_E_NFE: 0.6241%
- gnomAD_E_OTH: 1.0050%
- gnomAD_E_SAS: 0.7068%
- gnomAD_G_AFR: 0.5263%
- gnomAD_G_EAS: 0.4545%
- gnomAD_G_FIN: 0.0942%
- gnomAD_G_NFE: 0.6169%
- Pathogenicity Data:
- Best Score: 0.42299998
- SIFT: 0.577 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.531
- SIFT: 0.469 (T)
- Frequency Data:
- gnomAD_E_AFR: 0.0842%
- gnomAD_E_AMR: 0.8284%
- gnomAD_E_EAS: 1.0030%
- gnomAD_E_NFE: 0.1708%
- gnomAD_E_OTH: 0.6536%
- gnomAD_E_SAS: 0.2796%
- Pathogenicity Data:
- Best Score: 0.376
- SIFT: 0.624 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.49400002
- SIFT: 0.506 (T)
- Frequency Data:
- gnomAD_E_AFR: 0.0315%
- gnomAD_E_AMR: 0.0160%
- gnomAD_E_EAS: 0.0288%
- gnomAD_E_NFE: 0.0431%
- gnomAD_G_AFR: 0.7027%
- gnomAD_G_AMR: 1.1494%
- gnomAD_G_EAS: 0.8427%
- gnomAD_G_FIN: 0.1264%
- gnomAD_G_NFE: 0.5653%
- gnomAD_G_OTH: 1.0695%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_G_AFR: 1.4888%
- gnomAD_G_AMR: 1.6484%
- gnomAD_G_FIN: 1.0949%
- gnomAD_G_NFE: 1.5110%
- gnomAD_G_OTH: 0.6098%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_G_AFR: 1.5038%
- gnomAD_G_AMR: 1.6484%
- gnomAD_G_FIN: 1.0922%
- gnomAD_G_NFE: 1.5257%
- gnomAD_G_OTH: 0.6250%
- Pathogenicity Data:
- Best Score: 0.36699998
- SIFT: 0.633 (T)
- Frequency Data:
- gnomAD_G_AMR: 0.4808%
- gnomAD_G_EAS: 0.2273%
- gnomAD_G_FIN: 0.2927%
- gnomAD_G_NFE: 0.0677%
- gnomAD_G_OTH: 0.4405%
- Pathogenicity Data:
- Best Score: 0.269
- SIFT: 0.731 (T)
- Frequency Data:
- gnomAD_E_FIN: 0.0080%
- Pathogenicity Data:
- Best Score: 0.20899999
- SIFT: 0.791 (T)
- Frequency Data:
- 1000Genomes: 0.0599%
- TOPMed: 0.0599%
- gnomAD_E_AMR: 0.0045%
- gnomAD_E_NFE: 0.0018%
- gnomAD_E_SAS: 0.0057%
- Pathogenicity Data:
- Best Score: 0.877
- SIFT: 0.123 (T)
- Frequency Data:
- gnomAD_E_AFR: 0.0855%
- gnomAD_E_AMR: 0.1728%
- gnomAD_E_FIN: 0.3078%
- gnomAD_E_NFE: 0.5178%
- gnomAD_E_OTH: 0.2488%
- gnomAD_E_SAS: 1.0075%
- gnomAD_G_AFR: 1.5723%
- gnomAD_G_AMR: 1.7442%
- gnomAD_G_EAS: 0.5435%
- gnomAD_G_FIN: 1.4031%
- gnomAD_G_NFE: 1.7981%
- gnomAD_G_OTH: 1.9481%
- Pathogenicity Data:
- Best Score: 0.14600003
- SIFT: 0.854 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC NFE: 0.0123%
- gnomAD_E_AMR: 0.0045%
- gnomAD_E_NFE: 0.0093%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.2376%
- gnomAD_E_AMR: 0.4876%
- gnomAD_E_EAS: 0.2569%
- gnomAD_E_FIN: 0.1065%
- gnomAD_E_NFE: 0.2428%
- gnomAD_E_OTH: 0.1225%
- gnomAD_E_SAS: 0.1079%
- gnomAD_G_AFR: 0.2022%
- gnomAD_G_AMR: 0.4854%
- gnomAD_G_NFE: 0.1141%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_G_EAS: 0.7576%
- gnomAD_G_NFE: 0.0330%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0510%
- gnomAD_E_AMR: 0.0229%
- gnomAD_E_NFE: 0.0047%
- gnomAD_E_SAS: 0.0228%
- gnomAD_G_AFR: 0.4636%
- gnomAD_G_AMR: 1.2821%
- gnomAD_G_EAS: 0.2463%
- gnomAD_G_FIN: 0.2160%
- gnomAD_G_NFE: 0.4739%
- gnomAD_G_OTH: 0.7538%
- Pathogenicity Data:
- Best Score: 0.021000028
- SIFT: 0.979 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.0
- SIFT: 1.000 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.0
- SIFT: 1.000 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.0
- SIFT: 1.000 (T)
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 0.999977
- Mutation Taster: 1.000 (P)
- SIFT: 0.174 (T)
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
- Known diseases:
- ORPHA:269 Facioscapulohumeral dystrophy - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Transcripts:
- FRG1:ENST00000226798.4:c.604G>A:p.(Val202Ile)
- Pathogenicity Data:
- Best Score: 0.999968
- Polyphen2: 0.038 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.132 (T)
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 0.998
- Transcripts:
- FRG1:ENST00000226798.4:c.604G>A:p.(Val202Ile)
- Pathogenicity Data:
- Best Score: 0.999968
- Polyphen2: 0.038 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.132 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- FRG1:ENST00000226798.4:c.292A>T:p.(Thr98Ser)
- Pathogenicity Data:
- Best Score: 0.999999
- Polyphen2: 0.083 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.046 (D)
- Frequency Data:
- gnomAD_E_AFR: 0.0219%
- gnomAD_E_AMR: 0.0094%
- gnomAD_E_NFE: 0.0077%
- gnomAD_E_SAS: 0.0035%
- Transcripts:
- FRG1:ENST00000226798.4:c.322G>A:p.(Ala108Thr)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.241 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.038 (D)
- Frequency Data:
- TOPMed: 0.0019%
- ExAC FIN: 0.0303%
- ExAC NFE: 0.0075%
- ExAC SAS: 0.0121%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_SAS: 0.0098%
- Transcripts:
- FRG1:ENST00000226798.4:c.629+3A>G:p.?
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
- gnomAD_E_NFE: 0.0010%
- Transcripts:
- FRG1:ENST00000226798.4:c.627T>C:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
- gnomAD_E_OTH: 0.0204%
- Transcripts:
- FRG1:ENST00000226798.4:c.568A>G:p.(Lys190Glu)
- Pathogenicity Data:
- Best Score: 0.575598
- Polyphen2: 0.034 (B)
- Mutation Taster: 0.576
- SIFT: 0.615 (T)
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 0.99996
- Polyphen2: 0.997 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.003 (D)
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- TOPMed: 0.0004%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Transcripts:
- RP11-764K9.4:ENST00000376334.3:n.695+1G>A:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0004%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.007
Phenotype Score: 0.000
Variant Score: 0.900
- Transcripts:
- RP11-764K9.4:ENST00000376334.3:n.695+1G>A:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0004%
- Transcripts:
- RP11-764K9.4:ENST00000376334.3:n.785T>C:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- RP11-764K9.4:ENST00000376334.3:n.696-8A>T:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- RP11-764K9.4:ENST00000376334.3:n.695+3A>G:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- RP11-764K9.4:ENST00000376334.3:n.410_412del:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- RP11-764K9.4:ENST00000376334.3:n.412G>A:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0004%
- Transcripts:
- RP11-764K9.4:ENST00000376334.3:n.787+3A>G:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0045%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Transcripts:
- ANKRD20A1:ENST00000377477.2:c.203+1G>A:p.?
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 0.997
- Transcripts:
- ANKRD20A1:ENST00000377477.2:c.203+1G>A:p.?
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
- Transcripts:
- ANKRD20A1:ENST00000377477.2:c.190G>A:p.(Asp64Asn)
- Pathogenicity Data:
- Best Score: 0.995
- Polyphen2: 0.995 (D)
- Frequency Data:
- No frequency data
- Transcripts:
- ANKRD20A1:ENST00000377477.2:c.171C>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- ANKRD20A1:ENST00000377477.2:c.180G>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
X_RECESSIVE
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.271 (B)
- SIFT: 0.000 (D)
- Frequency Data:
- ExAC NFE: 0.0021%
- gnomAD_E_NFE: 0.0012%
X_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.271 (B)
- SIFT: 0.000 (D)
- Frequency Data:
- ExAC NFE: 0.0021%
- gnomAD_E_NFE: 0.0012%
- Pathogenicity Data:
- Best Score: 0.993
- Polyphen2: 0.760 (P)
- SIFT: 0.007 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.986
- Polyphen2: 0.062 (B)
- SIFT: 0.014 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC AFR: 0.4172%
- ExAC FIN: 0.0244%
- ExAC NFE: 0.0070%
- ExAC SAS: 0.0112%
- gnomAD_E_AFR: 0.0176%
- gnomAD_E_NFE: 0.0026%
- gnomAD_E_SAS: 0.0054%
- Pathogenicity Data:
- Best Score: 0.677
- Polyphen2: 0.677 (P)
- SIFT: 0.403 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.325
- Polyphen2: 0.001 (B)
- SIFT: 0.675 (T)
- Frequency Data:
- 1000Genomes: 0.1325%
- TOPMed: 0.1325%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 1.000
- Transcripts:
- TLNRD1:ENST00000267984.2:c.226G>C:p.(Glu76Gln)
- Pathogenicity Data:
- Best Score: 0.999999
- Polyphen2: 0.318 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.240 (T)
- Frequency Data:
- TOPMed: 0.0023%
- ExAC NFE: 0.0018%
- gnomAD_E_NFE: 0.0013%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 0.999
- Transcripts:
- PCDHA5:ENST00000378126.3:c.373A>G:p.(Ile125Val)
- PCDHA5:ENST00000529619.1:c.373A>G:p.(Ile125Val)
- PCDHA5:ENST00000529859.1:c.373A>G:p.(Ile125Val)
- PCDHA5:ENST00000512229.2:c.2385+12576A>G:p.(=)
- PCDHA5:ENST00000530339.1:c.2385+12576A>G:p.(=)
- PCDHA5:ENST00000526136.1:c.2388+24796A>G:p.(=)
- PCDHA5:ENST00000394633.3:c.1602+34256A>G:p.(=)
- PCDHA5:ENST00000504120.2:c.2394+33464A>G:p.(=)
- PCDHA5:ENST00000522353.2:c.2394+18557A>G:p.(=)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.017 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.261 (T)
- Frequency Data:
- gnomAD_E_EAS: 0.0058%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 0.999
- Transcripts:
- ANKRD20A4P:ENST00000357336.3:c.2088A>T:p.(Gln696His)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.001 (B)
- SIFT: 0.000 (D)
- Frequency Data:
- gnomAD_E_SAS: 0.0069%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.015
Phenotype Score: 0.000
Variant Score: 0.991
- Transcripts:
- ANKRD20A4P:ENST00000357336.3:c.2088A>T:p.(Gln696His)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.001 (B)
- SIFT: 0.000 (D)
- Frequency Data:
- gnomAD_E_SAS: 0.0069%
- Transcripts:
- ANKRD20A4P:ENST00000357336.3:c.1999A>C:p.(Thr667Pro)
- Pathogenicity Data:
- Best Score: 0.982
- Polyphen2: 0.009 (B)
- SIFT: 0.018 (D)
- Frequency Data:
- No frequency data
- Transcripts:
- ANKRD20A4P:ENST00000357336.3:c.1846G>T:p.(Ala616Ser)
- Pathogenicity Data:
- Best Score: 0.904
- Polyphen2: 0.662 (P)
- SIFT: 0.096 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- ANKRD20A4P:ENST00000357336.3:c.619G>A:p.(Val207Ile)
- Pathogenicity Data:
- Best Score: 0.549
- Polyphen2: 0.013 (B)
- SIFT: 0.451 (T)
- Frequency Data:
- gnomAD_G_AFR: 0.5743%
- gnomAD_G_AMR: 0.1678%
- gnomAD_G_FIN: 0.1068%
- gnomAD_G_NFE: 0.0338%
- gnomAD_G_OTH: 0.1319%
- Transcripts:
- ANKRD20A4P:ENST00000357336.3:c.622T>C:p.(Tyr208His)
- Pathogenicity Data:
- Best Score: 0.45499998
- Polyphen2: 0.000 (B)
- SIFT: 0.545 (T)
- Frequency Data:
- gnomAD_G_AFR: 0.6425%
- gnomAD_G_AMR: 0.3322%
- gnomAD_G_EAS: 0.0768%
- gnomAD_G_FIN: 0.0730%
- gnomAD_G_NFE: 0.0595%
- gnomAD_G_OTH: 0.1348%
- Transcripts:
- ANKRD20A4P:ENST00000357336.3:c.2051G>C:p.(Ser684Thr)
- Pathogenicity Data:
- Best Score: 0.288
- Polyphen2: 0.000 (B)
- SIFT: 0.712 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- ANKRD20A4P:ENST00000357336.3:c.1996G>A:p.(Glu666Lys)
- Pathogenicity Data:
- Best Score: 0.0
- Polyphen2: 0.000 (B)
- SIFT: 1.000 (T)
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 0.998
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.001 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.605 (T)
- Frequency Data:
- gnomAD_E_AMR: 0.0032%
- gnomAD_E_NFE: 0.0121%
- gnomAD_G_NFE: 0.0067%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 0.998
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.981 (D)
- Mutation Taster: 1.000 (P)
- Frequency Data:
- TOPMed: 0.0011%
- ExAC EAS: 0.0127%
- gnomAD_E_EAS: 0.0058%
- gnomAD_E_SAS: 0.0033%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.549
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.981 (D)
- Mutation Taster: 1.000 (P)
- Frequency Data:
- TOPMed: 0.0011%
- ExAC EAS: 0.0127%
- gnomAD_E_EAS: 0.0058%
- gnomAD_E_SAS: 0.0033%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
- gnomAD_G_AFR: 0.0120%
- Phenotypic similarity 0.403 to mouse mutant involving ST14.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0005650, abnormal limb bud morphology
- HP:0001363, Craniosynostosis - MP:0002092, abnormal eye morphology
- HP:0011304, Broad thumb - MP:0005650, abnormal limb bud morphology
- HP:0010055, Broad hallux - MP:0005650, abnormal limb bud morphology
- Proximity score 0.500 in interactome to MMP14 and phenotypic similarity 0.638 to Multicentric osteolysis-nodulosis-arthropathy spectrum associated with MMP14.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001230, Broad metacarpals
- HP:0001363, Craniosynostosis - HP:0005441, Sclerotic cranial sutures
- HP:0011304, Broad thumb - HP:0001230, Broad metacarpals
- HP:0010055, Broad hallux - HP:0006234, Osteolysis involving tarsal bones
- Proximity score 0.500 in interactome to MMP14 and phenotypic similarity 0.702 to mouse mutant of MMP14.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0003055, abnormal long bone epiphyseal plate morphology
- HP:0001363, Craniosynostosis - MP:0002835, abnormal cranial suture morphology
- HP:0011304, Broad thumb - MP:0003055, abnormal long bone epiphyseal plate morphology
- HP:0010055, Broad hallux - MP:0003055, abnormal long bone epiphyseal plate morphology
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:602400 Ichthyosis, congenital, autosomal recessive 11 - autosomal recessive
- ORPHA:91132 Ichthyosis-hypotrichosis syndrome - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.250
Variant Score: 0.715
- Transcripts:
- ST14:ENST00000278742.5:c.865G>A:p.(Ala289Thr)
- Pathogenicity Data:
- Best Score: 0.71500003
- Polyphen2: 0.063 (B)
- SIFT: 0.285 (T)
- Frequency Data:
- TOPMed: 0.0004%
- gnomAD_E_NFE: 0.0038%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 0.997
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.999 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.004 (D)
- Frequency Data:
- TOPMed: 0.0008%
- gnomAD_E_OTH: 0.0184%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 0.997
- Pathogenicity Data:
- Best Score: 0.999
- Polyphen2: 0.563 (P)
- Mutation Taster: 0.904
- SIFT: 0.001 (D)
- Frequency Data:
- TOPMed: 0.0008%
- ExAC SAS: 0.0125%
- gnomAD_E_SAS: 0.0042%
- No phenotype or PPI evidence
- Known diseases:
- OMIM:618074 ?Epilepsy, familial adult myoclonic, 6 (unconfirmed)
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 0.997
- Pathogenicity Data:
- Best Score: 0.997
- Polyphen2: 0.104 (B)
- SIFT: 0.003 (D)
- Frequency Data:
- TOPMed: 0.0008%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 0.996
- Transcripts:
- MOSMO:ENST00000562695.1:c.319_320insTGATCCTTTTCTGTATGGCTGCCCTAATATTTCCAATAGGATTTTACATCAAT:p.(Ser107Metfs*39)
- MOSMO:ENST00000567004.1:c.265_266insTGATCCTTTTCTGTATGGCTGCCCTAATATTTCCAATAGGATTTTACATCAAT:p.(Ser89Metfs*39)
- MOSMO:ENST00000542527.2:c.319_319+1insTGATCCTTTTCTGTATGGCTGCCCTAATATTTCCAATAGGATTTTACATCAAT:p.?
- MOSMO:ENST00000569656.1:c.250_250+1insTGATCCTTTTCTGTATGGCTGCCCTAATATTTCCAATAGGATTTTACATCAAT:p.?
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0138%
- gnomAD_E_NFE: 0.0176%
- gnomAD_E_OTH: 0.0266%
- gnomAD_E_SAS: 0.0176%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 0.996
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 1.000 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- TOPMed: 0.0008%
- ExAC EAS: 0.0242%
- gnomAD_E_EAS: 0.0315%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.016
Phenotype Score: 0.000
Variant Score: 0.995
- Pathogenicity Data:
- Best Score: 0.995
- Polyphen2: 0.995 (D)
- SIFT: 0.011 (D)
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.015
Phenotype Score: 0.000
Variant Score: 0.994
- Pathogenicity Data:
- Best Score: 0.995
- Polyphen2: 0.995 (D)
- SIFT: 0.011 (D)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.993
- Polyphen2: 0.993 (D)
- SIFT: 0.630 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.99
- Polyphen2: 0.990 (D)
- SIFT: 0.118 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.982
- Polyphen2: 0.724 (P)
- SIFT: 0.018 (D)
- Frequency Data:
- ExAC NFE: 0.0015%
- gnomAD_E_NFE: 0.0027%
- Pathogenicity Data:
- Best Score: 0.966
- Polyphen2: 0.966 (D)
- SIFT: 0.105 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.866
- SIFT: 0.134 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.848
- Polyphen2: 0.010 (B)
- SIFT: 0.152 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.491
- Polyphen2: 0.009 (B)
- SIFT: 0.509 (T)
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.004
- Polyphen2: 0.004 (B)
- Frequency Data:
- gnomAD_E_AMR: 0.0060%
- Pathogenicity Data:
- Best Score: 0.001
- Polyphen2: 0.001 (B)
- Frequency Data:
- ExAC NFE: 0.0015%
- gnomAD_E_NFE: 0.0009%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.015
Phenotype Score: 0.000
Variant Score: 0.995
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC AFR: 0.0390%
- ExAC EAS: 0.0118%
- ExAC NFE: 0.0305%
- ExAC SAS: 0.0188%
- Phenotypic similarity 0.285 to zebrafish mutant involving KNG1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - ZP:0019878, Meckel's cartilage truncated, abnormal
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Known diseases:
- OMIM:619363 Angioedema, hereditary, 6 - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.015
Phenotype Score: 0.285
Variant Score: 0.672
- Pathogenicity Data:
- Best Score: 0.676
- Polyphen2: 0.324 (B)
- SIFT: 0.324 (T)
- Frequency Data:
- TOPMed: 0.0004%
- ExAC EAS: 0.0466%
- gnomAD_E_EAS: 0.0232%
- No phenotype or PPI evidence
X_RECESSIVE
Exomiser Score: 0.015
Phenotype Score: 0.000
Variant Score: 0.994
- Transcripts:
- FAM47C:ENST00000358047.3:c.1255C>T:p.(Pro419Ser)
- Pathogenicity Data:
- Best Score: 0.994
- Polyphen2: 0.994 (D)
- SIFT: 0.489 (T)
- Frequency Data:
- No frequency data
X_DOMINANT
Exomiser Score: 0.015
Phenotype Score: 0.000
Variant Score: 0.994
- Transcripts:
- FAM47C:ENST00000358047.3:c.1255C>T:p.(Pro419Ser)
- Pathogenicity Data:
- Best Score: 0.994
- Polyphen2: 0.994 (D)
- SIFT: 0.489 (T)
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.015
Phenotype Score: 0.000
Variant Score: 0.994
- Pathogenicity Data:
- Best Score: 0.999366
- Polyphen2: 0.512 (P)
- Mutation Taster: 0.999 (P)
- SIFT: 0.171 (T)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0026%
- ExAC EAS: 0.0351%
- gnomAD_E_EAS: 0.0407%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.015
Phenotype Score: 0.000
Variant Score: 0.993
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.980 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.019 (D)
- Frequency Data:
- TOPMed: 0.0011%
- ExAC FIN: 0.0473%
- ExAC NFE: 0.0015%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_FIN: 0.0240%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_SAS: 0.0032%
- gnomAD_G_AFR: 0.0116%
- Proximity score 0.510 in interactome to FSTL1 and phenotypic similarity 0.735 to mouse mutant of FSTL1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis - MP:0020040, decreased bone ossification
- HP:0011304, Broad thumb - MP:0008730, fused phalanges
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.015
Phenotype Score: 0.510
Variant Score: 0.415
- Pathogenicity Data:
- Best Score: 0.99938
- Polyphen2: 0.934 (P)
- Mutation Taster: 0.999 (P)
- SIFT: 0.004 (D)
- Frequency Data:
- 1000Genomes: 0.1398%
- TOPMed: 0.0366%
- ExAC EAS: 1.0956%
- gnomAD_E_EAS: 1.0302%
- gnomAD_E_OTH: 0.0377%
- gnomAD_G_EAS: 1.0533%
- Transcripts:
- UTRN:ENST00000367545.3:c.7389G>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
- ExAC EAS: 0.0117%
- gnomAD_E_EAS: 0.0116%
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.510
Variant Score: 0.100
- Transcripts:
- UTRN:ENST00000367545.3:c.7389G>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
- ExAC EAS: 0.0117%
- gnomAD_E_EAS: 0.0116%
- No phenotype or PPI evidence
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:206100 Anemia, hypochromic microcytic, with iron overload 1 - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.015
Phenotype Score: 0.000
Variant Score: 0.991
- Transcripts:
- SLC11A2:ENST00000262051.7:c.1351C>T:p.(Pro451Ser)
- SLC11A2:ENST00000262052.5:c.1351C>T:p.(Pro451Ser)
- SLC11A2:ENST00000394904.3:c.1438C>T:p.(Pro480Ser)
- SLC11A2:ENST00000541174.2:c.1351C>T:p.(Pro451Ser)
- SLC11A2:ENST00000545993.2:c.1339C>T:p.(Pro447Ser)
- SLC11A2:ENST00000546743.1:c.1114C>T:p.(Pro372Ser)
- SLC11A2:ENST00000547198.1:c.1351C>T:p.(Pro451Ser)
- SLC11A2:ENST00000547688.1:c.1438C>T:p.(Pro480Ser)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 1.000 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0200%
- ExAC EAS: 0.0604%
- gnomAD_E_EAS: 0.0581%
- gnomAD_G_EAS: 0.0617%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.015
Phenotype Score: 0.000
Variant Score: 0.990
- Transcripts:
- SAMD1:ENST00000533683.2:c.538C>T:p.(Arg180Cys)
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.005 (B)
- Mutation Taster: 0.995 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- 1000Genomes: 0.0399%
- TOPMed: 0.0091%
- ExAC SAS: 0.0689%
- gnomAD_E_NFE: 0.0060%
- gnomAD_E_SAS: 0.0263%
- gnomAD_G_NFE: 0.0143%
- Phenotypic similarity 0.506 to Hypocalcemic vitamin D-dependent rickets associated with CYP2R1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0002970, Genu varum
- HP:0001363, Craniosynostosis - HP:0010537, Wide cranial sutures
- HP:0011304, Broad thumb - HP:0002982, Tibial bowing
- HP:0010055, Broad hallux - HP:0003029, Enlargement of the ankles
- Proximity score 0.504 in interactome to DHCR7 and phenotypic similarity 0.681 to Smith-Lemli-Opitz syndrome associated with DHCR7.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0004422, Biparietal narrowing
- HP:0011304, Broad thumb - HP:0009623, Proximal placement of thumb
- HP:0010055, Broad hallux - HP:0004691, 2-3 toe syndactyly
- Proximity score 0.504 in interactome to DHCR7 and phenotypic similarity 0.737 to mouse mutant of DHCR7.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000564, syndactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0000564, syndactyly
- HP:0010055, Broad hallux - MP:0000564, syndactyly
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:600081 Rickets due to defect in vitamin D 25-hydroxylation deficiency - autosomal recessive
- ORPHA:289157 Hypocalcemic vitamin D-dependent rickets - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.015
Phenotype Score: 0.252
Variant Score: 0.703
- Transcripts:
- CYP2R1:ENST00000334636.5:c.175T>C:p.(Ser59Pro)
- Pathogenicity Data:
- Best Score: 0.70500004
- Polyphen2: 0.006 (B)
- SIFT: 0.295 (T)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0004%
- gnomAD_E_EAS: 0.0058%
- Proximity score 0.501 in interactome to POLA1 and phenotypic similarity 0.625 to X-linked intellectual disability, Van Esch type associated with POLA1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0004209, Clinodactyly of the 5th finger
- HP:0001363, Craniosynostosis - HP:0004440, Coronal craniosynostosis
- HP:0011304, Broad thumb - HP:0004209, Clinodactyly of the 5th finger
- HP:0010055, Broad hallux - HP:0004209, Clinodactyly of the 5th finger
X_RECESSIVE
Exomiser Score: 0.015
Phenotype Score: 0.501
Variant Score: 0.420
- Pathogenicity Data:
- Best Score: 0.449
- Polyphen2: 0.027 (B)
- SIFT: 0.551 (T)
- Frequency Data:
- 1000Genomes: 0.0265%
- TOPMed: 0.0185%
- ExAC EAS: 0.2411%
- ExAC SAS: 0.0099%
- gnomAD_E_EAS: 0.2409%
- gnomAD_E_SAS: 0.0052%
- gnomAD_G_EAS: 0.3854%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.014
Phenotype Score: 0.000
Variant Score: 0.985
- Pathogenicity Data:
- Best Score: 0.994
- Polyphen2: 0.994 (D)
- SIFT: 0.009 (D)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0004%
- gnomAD_E_EAS: 0.0586%
- gnomAD_G_EAS: 0.0617%
- Phenotypic similarity 0.240 to mouse mutant involving EVA1C.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0002638, abnormal pupillary reflex
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.014
Phenotype Score: 0.240
Variant Score: 0.711
- Pathogenicity Data:
- Best Score: 0.71099997
- Polyphen2: 0.015 (B)
- SIFT: 0.289 (T)
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.013
Phenotype Score: 0.000
Variant Score: 0.979
- Pathogenicity Data:
- Best Score: 0.979
- Polyphen2: 0.008 (B)
- SIFT: 0.021 (D)
- Frequency Data:
- TOPMed: 0.0004%
- Phenotypic similarity 0.318 to mouse mutant involving ZNF407.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.011
Phenotype Score: 0.318
Variant Score: 0.600
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
- ExAC NFE: 0.0030%
- gnomAD_E_NFE: 0.0018%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.009
Phenotype Score: 0.000
Variant Score: 0.939
- Transcripts:
- POTEC:ENST00000358970.5:c.1516A>C:p.(Lys506Gln)
- Pathogenicity Data:
- Best Score: 0.939
- Polyphen2: 0.137 (B)
- SIFT: 0.061 (T)
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.005
Phenotype Score: 0.000
Variant Score: 0.862
- Transcripts:
- POTEC:ENST00000358970.5:c.1516A>C:p.(Lys506Gln)
- Pathogenicity Data:
- Best Score: 0.939
- Polyphen2: 0.137 (B)
- SIFT: 0.061 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- POTEC:ENST00000358970.5:c.1031A>G:p.(Tyr344Cys)
- Pathogenicity Data:
- Best Score: 0.998
- Polyphen2: 0.998 (D)
- SIFT: 0.007 (D)
- Frequency Data:
- TOPMed: 0.0404%
- gnomAD_E_EAS: 0.9464%
- gnomAD_E_SAS: 0.0136%
- gnomAD_G_EAS: 0.9375%
- Proximity score 0.500 in interactome to STAMBP and phenotypic similarity 0.666 to Microcephaly-capillary malformation syndrome associated with STAMBP.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009882, Short distal phalanx of finger
- HP:0010055, Broad hallux - HP:0030084, Clinodactyly
- Proximity score 0.500 in interactome to STAMBP and phenotypic similarity 0.268 to mouse mutant of STAMBP.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001344, blepharoptosis
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.009
Phenotype Score: 0.500
Variant Score: 0.368
- Pathogenicity Data:
- Best Score: 0.996
- Polyphen2: 0.056 (B)
- SIFT: 0.004 (D)
- Frequency Data:
- 1000Genomes: 0.3395%
- TOPMed: 0.2203%
- ESP AA: 0.3862%
- ESP EA: 0.0116%
- ESP All: 0.1385%
- ExAC AFR: 0.2759%
- ExAC AMR: 0.0346%
- ExAC EAS: 1.5552%
- ExAC NFE: 0.0046%
- ExAC OTH: 0.3341%
- ExAC SAS: 0.4931%
- gnomAD_E_AFR: 0.2755%
- gnomAD_E_AMR: 0.0273%
- gnomAD_E_EAS: 1.5382%
- gnomAD_E_NFE: 0.0054%
- gnomAD_E_OTH: 0.2033%
- gnomAD_E_SAS: 0.5660%
- gnomAD_G_AFR: 0.2754%
- gnomAD_G_AMR: 0.2387%
- gnomAD_G_EAS: 1.0481%
- gnomAD_G_NFE: 0.0067%
- gnomAD_G_OTH: 0.1020%
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.296 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.137 (T)
- Frequency Data:
- 1000Genomes: 0.5791%
- TOPMed: 0.1991%
- ESP AA: 0.1363%
- ESP EA: 0.0233%
- ESP All: 0.0616%
- ExAC AFR: 0.1445%
- ExAC AMR: 0.0432%
- ExAC EAS: 1.8848%
- ExAC NFE: 0.0075%
- ExAC OTH: 0.4415%
- ExAC SAS: 0.3696%
- gnomAD_E_AFR: 0.1372%
- gnomAD_E_AMR: 0.0357%
- gnomAD_E_EAS: 1.7683%
- gnomAD_E_FIN: 0.0045%
- gnomAD_E_NFE: 0.0090%
- gnomAD_E_OTH: 0.2007%
- gnomAD_E_SAS: 0.4256%
- gnomAD_G_AFR: 0.1953%
- gnomAD_G_AMR: 0.2387%
- gnomAD_G_EAS: 0.9271%
- gnomAD_G_NFE: 0.0201%
- gnomAD_G_OTH: 0.1020%
- Transcripts:
- CCDC88B:ENST00000356786.5:c.621G>C:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.3395%
- TOPMed: 0.2180%
- ESP AA: 0.3635%
- ESP EA: 0.0116%
- ESP All: 0.1308%
- ExAC AFR: 0.2819%
- ExAC AMR: 0.0353%
- ExAC EAS: 1.5585%
- ExAC NFE: 0.0048%
- ExAC OTH: 0.3817%
- ExAC SAS: 0.5178%
- gnomAD_E_AFR: 0.2741%
- gnomAD_E_AMR: 0.0277%
- gnomAD_E_EAS: 1.5260%
- gnomAD_E_NFE: 0.0056%
- gnomAD_E_OTH: 0.1701%
- gnomAD_E_SAS: 0.5276%
- gnomAD_G_AFR: 0.2880%
- gnomAD_G_AMR: 0.2392%
- gnomAD_G_EAS: 1.0533%
- gnomAD_G_NFE: 0.0067%
- gnomAD_G_OTH: 0.1033%
- Transcripts:
- CCDC88B:ENST00000356786.5:c.189C>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.2995%
- TOPMed: 0.1557%
- ESP AA: 0.0929%
- ESP EA: 0.0117%
- ESP All: 0.0390%
- ExAC AFR: 0.0430%
- ExAC AMR: 0.0348%
- ExAC EAS: 1.5789%
- ExAC NFE: 0.0047%
- ExAC OTH: 0.3480%
- ExAC SAS: 0.3821%
- gnomAD_E_AFR: 0.0594%
- gnomAD_E_AMR: 0.0270%
- gnomAD_E_EAS: 1.5352%
- gnomAD_E_NFE: 0.0056%
- gnomAD_E_OTH: 0.2038%
- gnomAD_E_SAS: 0.4014%
- gnomAD_G_AFR: 0.0575%
- gnomAD_G_AMR: 0.2387%
- gnomAD_G_EAS: 1.1111%
- gnomAD_G_NFE: 0.0067%
- gnomAD_G_OTH: 0.1025%
- No phenotype or PPI evidence
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.009
Phenotype Score: 0.000
Variant Score: 0.931
- Transcripts:
- POTED:ENST00000299443.5:c.337G>A:p.(Gly113Ser)
- Pathogenicity Data:
- Best Score: 0.937
- Polyphen2: 0.937 (P)
- SIFT: 0.153 (T)
- Frequency Data:
- gnomAD_E_AFR: 0.0481%
- gnomAD_E_NFE: 0.0078%
- gnomAD_E_SAS: 0.0092%
AUTOSOMAL_DOMINANT
Exomiser Score: 0.003
Phenotype Score: 0.000
Variant Score: 0.800
- Transcripts:
- POTED:ENST00000299443.5:c.918-4T>C:p.?
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- POTED:ENST00000299443.5:c.1603A>G:p.(Met535Val)
- Pathogenicity Data:
- Best Score: 0.78499997
- Polyphen2: 0.007 (B)
- SIFT: 0.215 (T)
- Frequency Data:
- No frequency data
- Transcripts:
- POTED:ENST00000299443.5:c.403A>G:p.(Ile135Val)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AMR: 0.1207%
- gnomAD_E_FIN: 0.0120%
- gnomAD_E_NFE: 0.0233%
- gnomAD_G_FIN: 0.0794%
- gnomAD_G_NFE: 0.0210%
- Transcripts:
- POTED:ENST00000299443.5:c.28A>G:p.(Thr10Ala)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_G_AFR: 0.1953%
- gnomAD_G_EAS: 1.6129%
- gnomAD_G_FIN: 0.2466%
- gnomAD_G_NFE: 0.0846%
- Transcripts:
- POTED:ENST00000299443.5:c.37A>G:p.(Thr13Ala)
- Pathogenicity Data:
- Best Score: 0.100000024
- SIFT: 0.900 (T)
- Frequency Data:
- No frequency data
- Proximity score 0.504 in interactome to COMT and phenotypic similarity 0.740 to 22q11.2 deletion syndrome associated with COMT.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001829, Foot polydactyly
- HP:0001363, Craniosynostosis - HP:0011324, Multiple suture craniosynostosis
- HP:0011304, Broad thumb - HP:0001161, Hand polydactyly
- HP:0010055, Broad hallux - HP:0001829, Foot polydactyly
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.008
Phenotype Score: 0.504
Variant Score: 0.357
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 1.000 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.000 (D)
- Frequency Data:
- 1000Genomes: 0.2995%
- TOPMed: 0.0359%
- ExAC AMR: 0.0087%
- ExAC EAS: 1.2500%
- ExAC SAS: 0.0061%
- gnomAD_E_EAS: 1.3451%
- gnomAD_E_OTH: 0.0182%
- gnomAD_G_EAS: 0.8642%
- gnomAD_G_NFE: 0.0067%
- gnomAD_G_OTH: 0.1018%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
- gnomAD_E_EAS: 0.0066%
- gnomAD_G_AMR: 0.1199%
- Phenotypic similarity 0.426 to Knobloch syndrome associated with COL18A1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - HP:0001362, Calvarial skull defect
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Phenotypic similarity 0.342 to mouse mutant involving COL18A1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001303, abnormal lens morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.509 in interactome to CTSK and phenotypic similarity 0.712 to Pycnodysostosis associated with CTSK.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0002645, Wormian bones
- HP:0011304, Broad thumb - HP:0009839, Osteolytic defects of the distal phalanges of the hand
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Proximity score 0.509 in interactome to CTSK and phenotypic similarity 0.698 to mouse mutant of CTSK.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0005306, abnormal phalanx morphology
- HP:0001363, Craniosynostosis - MP:0030029, wide cranial sutures
- HP:0011304, Broad thumb - MP:0005306, abnormal phalanx morphology
- HP:0010055, Broad hallux - MP:0005306, abnormal phalanx morphology
- Known diseases:
- OMIM:267750 Knobloch syndrome, type 1 - autosomal recessive
- OMIM:618880 Glaucoma, primary closed-angle - autosomal dominant
- ORPHA:1571 Knobloch syndrome - autosomal recessive
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.008
Phenotype Score: 0.509
Variant Score: 0.345
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.426 to ORPHA:1571 Knobloch syndrome
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ESP AA: 0.1488%
- ESP EA: 0.2895%
- ESP All: 0.2464%
- ExAC AFR: 0.0565%
- ExAC AMR: 0.0140%
- ExAC EAS: 0.2064%
- ExAC FIN: 0.0229%
- ExAC NFE: 0.1054%
- ExAC SAS: 0.1092%
- gnomAD_E_AFR: 0.0430%
- gnomAD_E_AMR: 0.0337%
- gnomAD_E_EAS: 0.2364%
- gnomAD_E_FIN: 0.0187%
- gnomAD_E_NFE: 0.0931%
- gnomAD_E_OTH: 0.1179%
- gnomAD_E_SAS: 0.1207%
- gnomAD_G_AFR: 0.0807%
- gnomAD_G_EAS: 0.9877%
- gnomAD_G_NFE: 0.1943%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 1.7770%
- TOPMed: 0.4922%
- ESP AA: 0.0847%
- ESP All: 0.0259%
- ExAC AFR: 1.3370%
- ExAC AMR: 0.0794%
- ExAC EAS: 1.6159%
- ExAC NFE: 0.0252%
- ExAC OTH: 0.4601%
- ExAC SAS: 0.0138%
- gnomAD_E_AFR: 1.1691%
- gnomAD_E_AMR: 0.0758%
- gnomAD_E_EAS: 1.4811%
- gnomAD_E_NFE: 0.0220%
- gnomAD_E_OTH: 0.1177%
- gnomAD_E_SAS: 0.0267%
- gnomAD_G_AFR: 1.3263%
- gnomAD_G_AMR: 0.2410%
- gnomAD_G_EAS: 1.4180%
- gnomAD_G_NFE: 0.0067%
- gnomAD_G_OTH: 0.5165%
- Phenotypic similarity 0.286 to mouse mutant involving FCGBP.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0002092, abnormal eye morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.008
Phenotype Score: 0.286
Variant Score: 0.595
- Transcripts:
- FCGBP:ENST00000221347.6:c.1201G>T:p.(Ala401Ser)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0004%
- ExAC EAS: 0.0234%
- gnomAD_E_EAS: 0.0180%
- gnomAD_G_EAS: 0.0617%
- No phenotype or PPI evidence
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.007
Phenotype Score: 0.000
Variant Score: 0.903
- Pathogenicity Data:
- Best Score: 0.903
- Polyphen2: 0.010 (B)
- SIFT: 0.097 (T)
- Frequency Data:
- No frequency data
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- Best Score: 0.666
- Polyphen2: 0.074 (B)
- SIFT: 0.334 (T)
- Frequency Data:
- 1000Genomes: 0.2596%
- TOPMed: 0.2596%
- ExAC EAS: 0.1058%
- ExAC NFE: 0.0045%
- gnomAD_E_EAS: 0.0180%
- gnomAD_E_NFE: 0.0054%
- gnomAD_G_AFR: 0.1516%
- gnomAD_G_AMR: 0.2410%
- gnomAD_G_EAS: 0.4642%
- gnomAD_G_NFE: 0.0067%
- Pathogenicity Data:
- Best Score: 0.607
- SIFT: 0.393 (T)
- Frequency Data:
- 1000Genomes: 0.3195%
- TOPMed: 0.3195%
- ExAC EAS: 0.1647%
- ExAC NFE: 0.0030%
- gnomAD_E_EAS: 0.0479%
- gnomAD_E_NFE: 0.0045%
- gnomAD_G_AFR: 0.1166%
- gnomAD_G_AMR: 0.2398%
- gnomAD_G_EAS: 0.5277%
- gnomAD_G_NFE: 0.0067%
- Pathogenicity Data:
- Best Score: 0.41500002
- SIFT: 0.585 (T)
- Frequency Data:
- 1000Genomes: 0.3195%
- TOPMed: 0.3195%
- ExAC EAS: 0.1646%
- ExAC NFE: 0.0030%
- gnomAD_E_EAS: 0.1085%
- gnomAD_E_NFE: 0.0045%
- gnomAD_G_AFR: 0.1164%
- gnomAD_G_AMR: 0.2404%
- gnomAD_G_EAS: 0.5256%
- gnomAD_G_NFE: 0.0067%
- No phenotype or PPI evidence
X_RECESSIVE
Exomiser Score: 0.006
Phenotype Score: 0.000
Variant Score: 0.898
- Transcripts:
- ZNF185:ENST00000318504.7:c.916G>A:p.(Val306Ile)
- ZNF185:ENST00000318529.8:c.430G>A:p.(Val144Ile)
- ZNF185:ENST00000370268.4:c.1093G>A:p.(Val365Ile)
- ZNF185:ENST00000370270.2:c.1093G>A:p.(Val365Ile)
- ZNF185:ENST00000449285.2:c.1096G>A:p.(Val366Ile)
- ZNF185:ENST00000535861.1:c.1093G>A:p.(Val365Ile)
- ZNF185:ENST00000539731.1:c.1006G>A:p.(Val336Ile)
- ZNF185:ENST00000324823.6:c.422+4285G>A:p.(=)
- Pathogenicity Data:
- Best Score: 0.929
- Polyphen2: 0.059 (B)
- SIFT: 0.071 (T)
- Frequency Data:
- TOPMed: 0.0068%
- ExAC EAS: 0.2218%
- gnomAD_E_EAS: 0.1415%
- gnomAD_E_OTH: 0.0276%
- gnomAD_G_EAS: 0.0966%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.006
Phenotype Score: 0.000
Variant Score: 0.896
- Pathogenicity Data:
- Best Score: 0.904
- Polyphen2: 0.003 (B)
- SIFT: 0.096 (T)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0008%
- gnomAD_G_EAS: 0.0617%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.003
Phenotype Score: 0.000
Variant Score: 0.826
- Pathogenicity Data:
- Best Score: 0.904
- Polyphen2: 0.003 (B)
- SIFT: 0.096 (T)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0008%
- gnomAD_G_EAS: 0.0617%
- Pathogenicity Data:
- Best Score: 0.936815
- Polyphen2: 0.001 (B)
- Mutation Taster: 0.937
- SIFT: 0.211 (T)
- Frequency Data:
- 1000Genomes: 0.0599%
- TOPMed: 0.0144%
- ESP EA: 0.0116%
- ESP All: 0.0077%
- ExAC EAS: 0.1047%
- ExAC FIN: 0.8862%
- ExAC NFE: 0.0647%
- ExAC OTH: 0.1333%
- ExAC SAS: 0.0067%
- gnomAD_E_EAS: 0.0407%
- gnomAD_E_FIN: 0.7570%
- gnomAD_E_NFE: 0.0318%
- gnomAD_E_OTH: 0.1112%
- gnomAD_E_SAS: 0.0065%
- gnomAD_G_EAS: 0.0617%
- gnomAD_G_FIN: 0.7450%
- gnomAD_G_NFE: 0.0804%
- gnomAD_G_OTH: 0.2049%
- Proximity score 0.500 in interactome to GNAS and phenotypic similarity 0.784 to Pseudohypoparathyroidism type 1A associated with GNAS.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0002684, Thickened calvaria
- HP:0011304, Broad thumb - HP:0009642, Broad distal phalanx of the thumb
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Proximity score 0.500 in interactome to GNAS and phenotypic similarity 0.497 to mouse mutant of GNAS.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0003109, short femur
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb - MP:0003109, short femur
- HP:0010055, Broad hallux - MP:0003109, short femur
AUTOSOMAL_DOMINANT
Exomiser Score: 0.005
Phenotype Score: 0.500
Variant Score: 0.309
- Pathogenicity Data:
- Best Score: 0.31
- Polyphen2: 0.023 (B)
- SIFT: 0.690 (T)
- Frequency Data:
- TOPMed: 0.0008%
- ExAC EAS: 0.0116%
- gnomAD_E_EAS: 0.0174%
- Phenotypic similarity 0.306 to mouse mutant involving NAALADL2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0002092, abnormal eye morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.004
Phenotype Score: 0.306
Variant Score: 0.504
- Transcripts:
- NAALADL2:ENST00000454872.1:c.1193C>A:p.(Thr398Asn)
- Pathogenicity Data:
- Best Score: 0.504
- Polyphen2: 0.001 (B)
- SIFT: 0.496 (T)
- Frequency Data:
- TOPMed: 0.0004%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.004
Phenotype Score: 0.000
Variant Score: 0.850
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.004
Phenotype Score: 0.000
Variant Score: 0.850
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.004
Phenotype Score: 0.000
Variant Score: 0.850
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.004
Phenotype Score: 0.000
Variant Score: 0.850
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.663 to Acrodysostosis with multiple hormone resistance associated with PDE4D.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009803, Short phalanx of finger
- HP:0010055, Broad hallux - HP:0001831, Short toe
- Known diseases:
- OMIM:614613 Acrodysostosis 2, with or without hormone resistance - autosomal dominant
- ORPHA:280651 Acrodysostosis with multiple hormone resistance - autosomal dominant
- ORPHA:950 Acrodysostosis - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.004
Phenotype Score: 0.663
Variant Score: 0.099
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.663 to ORPHA:280651 Acrodysostosis with multiple hormone resistance
- Phenotypic similarity 0.656 to ORPHA:950 Acrodysostosis
- Phenotypic similarity 0.654 to OMIM:614613 Acrodysostosis 2, with or without hormone resistance
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0026%
- gnomAD_G_EAS: 0.0619%
- Phenotypic similarity 0.741 to Macrocephaly-developmental delay syndrome associated with KPTN.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0004209, Clinodactyly of the 5th finger
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0004209, Clinodactyly of the 5th finger
- HP:0010055, Broad hallux - HP:0004209, Clinodactyly of the 5th finger
- Phenotypic similarity 0.318 to mouse mutant involving KPTN.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:615637 Mental retardation, autosomal recessive 41 - autosomal recessive
- ORPHA:397612 Macrocephaly-developmental delay syndrome - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.159
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0024%
- ExAC EAS: 0.0352%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_EAS: 0.0523%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.004
Phenotype Score: 0.000
Variant Score: 0.833
- Pathogenicity Data:
- Best Score: 0.833
- Polyphen2: 0.718 (P)
- SIFT: 0.167 (T)
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.590 to Heart and brain malformation syndrome associated with SMG9.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0100490, Camptodactyly of finger
- HP:0001363, Craniosynostosis - HP:0005487, Prominent metopic ridge
- HP:0011304, Broad thumb - HP:0100490, Camptodactyly of finger
- HP:0010055, Broad hallux - HP:0100490, Camptodactyly of finger
- Phenotypic similarity 0.736 to mouse mutant involving SMG9.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0009743, preaxial polydactyly
- HP:0001363, Craniosynostosis - MP:0001297, microphthalmia
- HP:0011304, Broad thumb - MP:0009743, preaxial polydactyly
- HP:0010055, Broad hallux - MP:0009743, preaxial polydactyly
- Proximity score 0.501 in interactome to RPL27 and phenotypic similarity 0.670 to Blackfan-Diamond anemia associated with RPL27.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0009778, Short thumb
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001199, Triphalangeal thumb
- HP:0010055, Broad hallux - HP:0001199, Triphalangeal thumb
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:616920 Heart and brain malformation syndrome - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.368
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC SAS: 0.0182%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_SAS: 0.0162%
- No phenotype or PPI evidence
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.004
Phenotype Score: 0.000
Variant Score: 0.832
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0348%
- gnomAD_E_AMR: 0.2382%
- gnomAD_E_EAS: 0.0103%
- gnomAD_E_FIN: 0.1303%
- gnomAD_E_NFE: 0.3321%
- gnomAD_E_OTH: 0.3049%
- gnomAD_E_SAS: 0.0802%
- gnomAD_G_AFR: 0.0476%
- gnomAD_G_AMR: 0.1279%
- gnomAD_G_EAS: 0.1882%
- gnomAD_G_NFE: 0.2690%
- gnomAD_G_OTH: 0.2183%
- Transcripts:
- MUC22:ENST00000561890.1:c.1671G>A:p.(Met557Ile)
- Pathogenicity Data:
- Best Score: 0.909
- SIFT: 0.091 (T)
- Frequency Data:
- 1000Genomes: 0.9385%
- TOPMed: 0.9385%
- gnomAD_E_AFR: 0.6878%
- gnomAD_E_AMR: 0.4289%
- gnomAD_E_EAS: 0.3625%
- gnomAD_E_FIN: 0.1513%
- gnomAD_E_NFE: 0.5904%
- gnomAD_E_OTH: 0.5532%
- gnomAD_E_SAS: 0.1038%
- gnomAD_G_AFR: 0.6377%
- gnomAD_G_AMR: 0.3947%
- gnomAD_G_EAS: 0.1951%
- gnomAD_G_FIN: 0.0311%
- gnomAD_G_NFE: 0.4824%
- gnomAD_G_OTH: 0.3488%
- Transcripts:
- MUC22:ENST00000561890.1:c.211A>G:p.(Thr71Ala)
- Pathogenicity Data:
- Best Score: 0.61
- SIFT: 0.390 (T)
- Frequency Data:
- 1000Genomes: 0.4593%
- TOPMed: 0.1949%
- UK10K: 0.0661%
- ExAC NFE: 0.5654%
- ExAC SAS: 0.0534%
- gnomAD_E_AFR: 0.0853%
- gnomAD_E_AMR: 0.5208%
- gnomAD_E_EAS: 1.0548%
- gnomAD_E_FIN: 0.0189%
- gnomAD_E_NFE: 0.0775%
- gnomAD_E_OTH: 0.2576%
- gnomAD_E_SAS: 0.0490%
- gnomAD_G_AFR: 0.0690%
- gnomAD_G_AMR: 0.4773%
- gnomAD_G_EAS: 0.2472%
- gnomAD_G_NFE: 0.0869%
- Transcripts:
- MUC22:ENST00000561890.1:c.4067C>G:p.(Thr1356Arg)
- Pathogenicity Data:
- Best Score: 0.897
- SIFT: 0.103 (T)
- Frequency Data:
- 1000Genomes: 0.9984%
- TOPMed: 1.1600%
- UK10K: 0.5157%
- ExAC AFR: 1.5957%
- ExAC NFE: 0.5499%
- ExAC SAS: 0.1866%
- gnomAD_E_AFR: 1.7188%
- gnomAD_E_AMR: 0.6434%
- gnomAD_E_EAS: 1.0870%
- gnomAD_E_FIN: 0.2267%
- gnomAD_E_NFE: 0.9553%
- gnomAD_E_OTH: 1.0321%
- gnomAD_E_SAS: 0.1693%
- gnomAD_G_AFR: 1.7376%
- gnomAD_G_AMR: 0.4773%
- gnomAD_G_EAS: 0.2481%
- gnomAD_G_FIN: 0.0574%
- gnomAD_G_NFE: 0.9964%
- gnomAD_G_OTH: 0.7187%
- Transcripts:
- MUC22:ENST00000561890.1:c.1670T>C:p.(Met557Thr)
- Pathogenicity Data:
- Best Score: 0.35799998
- SIFT: 0.642 (T)
- Frequency Data:
- gnomAD_E_AFR: 0.6881%
- gnomAD_E_AMR: 0.4515%
- gnomAD_E_EAS: 0.3624%
- gnomAD_E_FIN: 0.1942%
- gnomAD_E_NFE: 0.5975%
- gnomAD_E_OTH: 0.5832%
- gnomAD_E_SAS: 0.1039%
- gnomAD_G_AFR: 0.6418%
- gnomAD_G_AMR: 0.3927%
- gnomAD_G_EAS: 0.1940%
- gnomAD_G_FIN: 0.0310%
- gnomAD_G_NFE: 0.4875%
- gnomAD_G_OTH: 0.3488%
- Transcripts:
- MUC22:ENST00000561890.1:c.1024A>G:p.(Met342Val)
- Pathogenicity Data:
- Best Score: 0.13499999
- SIFT: 0.865 (T)
- Frequency Data:
- 1000Genomes: 0.5791%
- TOPMed: 0.5791%
- UK10K: 0.5290%
- ExAC AFR: 0.5263%
- ExAC NFE: 0.6886%
- ExAC SAS: 0.2089%
- gnomAD_E_AFR: 0.2236%
- gnomAD_E_AMR: 0.6378%
- gnomAD_E_EAS: 1.1623%
- gnomAD_E_FIN: 0.2587%
- gnomAD_E_NFE: 1.0961%
- gnomAD_E_OTH: 1.1710%
- gnomAD_E_SAS: 0.1863%
- gnomAD_G_AFR: 0.2950%
- gnomAD_G_AMR: 0.3817%
- gnomAD_G_EAS: 0.2522%
- gnomAD_G_FIN: 0.0606%
- gnomAD_G_NFE: 1.0753%
- gnomAD_G_OTH: 0.6593%
- Transcripts:
- MUC22:ENST00000561890.1:c.1668T>C:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.9984%
- TOPMed: 0.9984%
- gnomAD_E_AFR: 0.7052%
- gnomAD_E_AMR: 0.4500%
- gnomAD_E_EAS: 0.3628%
- gnomAD_E_FIN: 0.2160%
- gnomAD_E_NFE: 0.6163%
- gnomAD_E_OTH: 0.6146%
- gnomAD_E_SAS: 0.1039%
- gnomAD_G_AFR: 0.6429%
- gnomAD_G_AMR: 0.3866%
- gnomAD_G_EAS: 0.1926%
- gnomAD_G_FIN: 0.0307%
- gnomAD_G_NFE: 0.5068%
- gnomAD_G_OTH: 0.3409%
- Transcripts:
- MUC22:ENST00000561890.1:c.1570A>G:p.(Lys524Glu)
- Pathogenicity Data:
- Best Score: 0.0
- SIFT: 1.000 (T)
- Frequency Data:
- 1000Genomes: 0.9984%
- TOPMed: 0.9984%
- UK10K: 0.5554%
- ExAC AFR: 1.5957%
- ExAC NFE: 0.7645%
- ExAC SAS: 0.2083%
- gnomAD_E_AFR: 1.7562%
- gnomAD_E_AMR: 0.7959%
- gnomAD_E_EAS: 1.1526%
- gnomAD_E_FIN: 0.2579%
- gnomAD_E_NFE: 1.1191%
- gnomAD_E_OTH: 1.1417%
- gnomAD_E_SAS: 0.1863%
- gnomAD_G_AFR: 1.7490%
- gnomAD_G_AMR: 0.5141%
- gnomAD_G_EAS: 0.2513%
- gnomAD_G_FIN: 0.0305%
- gnomAD_G_NFE: 1.1230%
- gnomAD_G_OTH: 0.8734%
- Phenotypic similarity 0.552 to mouse mutant involving TTC28.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0004509, abnormal pelvic girdle bone morphology
- HP:0001363, Craniosynostosis - MP:0004609, vertebral fusion
- HP:0011304, Broad thumb - MP:0004509, abnormal pelvic girdle bone morphology
- HP:0010055, Broad hallux - MP:0004509, abnormal pelvic girdle bone morphology
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.003
Phenotype Score: 0.552
Variant Score: 0.198
- Transcripts:
- TTC28:ENST00000397906.2:c.76C>A:p.(Pro26Thr)
- Pathogenicity Data:
- Best Score: 0.853
- Polyphen2: 0.014 (B)
- SIFT: 0.147 (T)
- Frequency Data:
- ExAC SAS: 0.0189%
- gnomAD_E_AMR: 0.1508%
- gnomAD_E_EAS: 0.5597%
- gnomAD_E_FIN: 0.0271%
- gnomAD_E_NFE: 0.0238%
- gnomAD_E_OTH: 0.1422%
- gnomAD_E_SAS: 0.0449%
- gnomAD_G_AFR: 0.1916%
- gnomAD_G_AMR: 1.0234%
- gnomAD_G_EAS: 0.0657%
- gnomAD_G_FIN: 1.6406%
- gnomAD_G_NFE: 0.0556%
- gnomAD_G_OTH: 0.2212%
- Transcripts:
- TTC28:ENST00000397906.2:c.78A>C:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AMR: 0.1421%
- gnomAD_E_EAS: 0.3257%
- gnomAD_E_FIN: 0.0517%
- gnomAD_E_NFE: 0.0273%
- gnomAD_E_OTH: 0.1979%
- gnomAD_E_SAS: 0.0430%
- gnomAD_G_AFR: 0.2551%
- gnomAD_G_AMR: 1.0938%
- gnomAD_G_EAS: 0.2199%
- gnomAD_G_FIN: 1.9108%
- gnomAD_G_NFE: 0.1018%
- gnomAD_G_OTH: 0.2370%
- Proximity score 0.501 in interactome to ANTXR2 and phenotypic similarity 0.651 to Infantile systemic hyalinosis associated with ANTXR2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0100490, Camptodactyly of finger
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.003
Phenotype Score: 0.501
Variant Score: 0.251
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.1198%
- TOPMed: 0.0932%
- ExAC EAS: 1.1714%
- ExAC SAS: 0.0063%
- gnomAD_E_EAS: 1.2929%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_OTH: 0.0366%
- gnomAD_E_SAS: 0.0065%
- gnomAD_G_EAS: 1.5432%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC SAS: 0.0062%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_SAS: 0.0033%
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.501
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC SAS: 0.0062%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_SAS: 0.0033%
- Proximity score 0.503 in interactome to IRF6 and phenotypic similarity 0.533 to Autosomal dominant popliteal pterygium syndrome associated with IRF6.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001770, Toe syndactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0006101, Finger syndactyly
- HP:0010055, Broad hallux - HP:0001770, Toe syndactyly
- Proximity score 0.503 in interactome to IRF6 and phenotypic similarity 0.715 to mouse mutant of IRF6.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis - MP:0000060, delayed bone ossification
- HP:0011304, Broad thumb - MP:0005306, abnormal phalanx morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.003
Phenotype Score: 0.503
Variant Score: 0.248
- Transcripts:
- SP100:ENST00000264052.5:c.16G>A:p.(Gly6Ser)
- SP100:ENST00000340126.4:c.16G>A:p.(Gly6Ser)
- SP100:ENST00000341950.4:c.16G>A:p.(Gly6Ser)
- SP100:ENST00000409112.1:c.16G>A:p.(Gly6Ser)
- SP100:ENST00000409341.1:c.16G>A:p.(Gly6Ser)
- SP100:ENST00000409824.1:c.16G>A:p.(Gly6Ser)
- SP100:ENST00000427101.2:c.16G>A:p.(Gly6Ser)
- Pathogenicity Data:
- Best Score: 0.436
- Polyphen2: 0.002 (B)
- SIFT: 0.564 (T)
- Frequency Data:
- 1000Genomes: 0.0998%
- TOPMed: 0.0155%
- ExAC EAS: 0.4600%
- gnomAD_E_EAS: 0.4531%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_OTH: 0.0184%
- gnomAD_E_SAS: 0.0065%
- gnomAD_G_EAS: 0.4326%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0599%
- TOPMed: 0.0191%
- ExAC EAS: 0.2661%
- gnomAD_E_EAS: 0.3711%
- gnomAD_E_OTH: 0.0183%
- gnomAD_G_EAS: 0.3717%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.003
Phenotype Score: 0.000
Variant Score: 0.814
- Pathogenicity Data:
- Best Score: 0.81406
- Polyphen2: 0.001 (B)
- Mutation Taster: 0.814
- SIFT: 1.000 (T)
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.003
Phenotype Score: 0.000
Variant Score: 0.806
- Pathogenicity Data:
- Best Score: 0.806
- SIFT: 0.194 (T)
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
X_RECESSIVE
Exomiser Score: 0.003
Phenotype Score: 0.000
Variant Score: 0.805
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC EAS: 0.2294%
- gnomAD_G_EAS: 0.3279%
- gnomAD_G_NFE: 0.0104%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.003
Phenotype Score: 0.000
Variant Score: 0.805
- Pathogenicity Data:
- Best Score: 0.805
- Polyphen2: 0.004 (B)
- SIFT: 0.195 (T)
- Frequency Data:
- gnomAD_E_FIN: 0.0045%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.003
Phenotype Score: 0.000
Variant Score: 0.800
- Transcripts:
- BAGE2:ENST00000470054.1:n.1714-5_1714-4insT:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.003
Phenotype Score: 0.000
Variant Score: 0.800
- Transcripts:
- BAGE2:ENST00000470054.1:n.1714-5_1714-4insT:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- BAGE2:ENST00000470054.1:n.1596+4C>A:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- BAGE2:ENST00000470054.1:n.1476+6G>T:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- BAGE2:ENST00000470054.1:n.203_222del:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.003
Phenotype Score: 0.000
Variant Score: 0.800
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.003
Phenotype Score: 0.000
Variant Score: 0.800
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.003
Phenotype Score: 0.000
Variant Score: 0.800
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.003
Phenotype Score: 0.000
Variant Score: 0.800
- Transcripts:
- RP11-391M20.1:ENST00000427066.1:n.62-6T>G:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.003
Phenotype Score: 0.000
Variant Score: 0.800
- Transcripts:
- RP11-391M20.1:ENST00000427066.1:n.62-6T>G:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Transcripts:
- RP11-391M20.1:ENST00000427066.1:n.123C>T:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.003
Phenotype Score: 0.000
Variant Score: 0.800
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.003
Phenotype Score: 0.000
Variant Score: 0.800
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
- Known diseases:
- OMIM:618734 ?Aneurysm, intracranial berry, 12 (unconfirmed)
- ORPHA:231160 Familial cerebral saccular aneurysm - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.003
Phenotype Score: 0.000
Variant Score: 0.800
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0004%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.003
Phenotype Score: 0.000
Variant Score: 0.799
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
- gnomAD_E_EAS: 0.0096%
- Phenotypic similarity 0.333 to Dihydropyrimidine dehydrogenase deficiency associated with DPYD.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001799, Short nail
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0002656, Epiphyseal dysplasia
- HP:0010055, Broad hallux - HP:0001799, Short nail
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:274270 Dihydropyrimidine dehydrogenase deficiency - autosomal recessive
- ORPHA:1675 Dihydropyrimidine dehydrogenase deficiency - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.002
Phenotype Score: 0.000
Variant Score: 0.795
- Transcripts:
- DPYD:ENST00000370192.3:c.1905C>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0253%
- UK10K: 0.0264%
- ESP EA: 0.0465%
- ESP All: 0.0308%
- ExAC AMR: 0.0087%
- ExAC NFE: 0.0480%
- ExAC SAS: 0.0182%
- gnomAD_E_AMR: 0.0060%
- gnomAD_E_NFE: 0.0188%
- gnomAD_E_OTH: 0.0365%
- gnomAD_E_SAS: 0.0162%
- gnomAD_G_NFE: 0.0133%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.002
Phenotype Score: 0.000
Variant Score: 0.793
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0004%
- gnomAD_G_EAS: 0.0618%
- No phenotype or PPI evidence
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.002
Phenotype Score: 0.000
Variant Score: 0.788
- Transcripts:
- ZNF815P:ENST00000421890.1:n.471A>G:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_G_EAS: 0.0646%
- gnomAD_G_FIN: 0.0304%
- gnomAD_G_NFE: 0.0206%
- gnomAD_G_OTH: 0.1073%
- Transcripts:
- ZNF815P:ENST00000421890.1:n.473A>G:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_G_AFR: 0.0241%
- gnomAD_G_EAS: 0.0643%
- gnomAD_G_FIN: 0.0305%
- gnomAD_G_NFE: 0.0275%
- gnomAD_G_OTH: 0.1073%
- Phenotypic similarity 0.693 to Mucolipidosis III alpha/beta associated with GNPTAB.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0006162, Soft tissue swelling of interphalangeal joints
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0006162, Soft tissue swelling of interphalangeal joints
- HP:0010055, Broad hallux - HP:0006162, Soft tissue swelling of interphalangeal joints
- Phenotypic similarity 0.482 to mouse mutant involving GNPTAB.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0006395, abnormal epiphyseal plate morphology
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb - MP:0006395, abnormal epiphyseal plate morphology
- HP:0010055, Broad hallux - MP:0006395, abnormal epiphyseal plate morphology
- Phenotypic similarity 0.463 to zebrafish mutant involving GNPTAB.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - ZP:0019548, endochondral bone decreased occurrence ossification, abnormal
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.500 in interactome to FURIN and phenotypic similarity 0.935 to mouse mutant of FURIN.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002544, brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002544, brachydactyly
- HP:0010055, Broad hallux - MP:0002544, brachydactyly
- Proximity score 0.500 in interactome to FURIN and phenotypic similarity 0.274 to fish mutant of FURIN.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - ZP:0006947, symplectic in contact with Meckel's cartilage, abnormal
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:252500 Mucolipidosis II alpha/beta - autosomal recessive
- OMIM:252600 Mucolipidosis III alpha/beta - autosomal recessive
- ORPHA:576 Mucolipidosis type II - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.250
Variant Score: 0.000
- Transcripts:
- GNPTAB:ENST00000299314.7:c.2504C>T:p.(Pro835Leu)
- Pathogenicity Data:
- Best Score: 0.0
- Polyphen2: 0.000 (B)
- SIFT: 1.000 (T)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0023%
- ExAC EAS: 0.0579%
- gnomAD_E_EAS: 0.0697%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.002
Phenotype Score: 0.000
Variant Score: 0.768
- Transcripts:
- CASP5:ENST00000260315.3:c.205G>A:p.(Val69Ile)
- CASP5:ENST00000393139.2:c.106G>A:p.(Val36Ile)
- CASP5:ENST00000393141.2:c.244G>A:p.(Val82Ile)
- CASP5:ENST00000444749.2:c.31G>A:p.(Val11Ile)
- CASP5:ENST00000526056.1:c.244G>A:p.(Val82Ile)
- CASP5:ENST00000418434.1:c.8-3928G>A:p.(=)
- CASP5:ENST00000531367.1:c.8-3928G>A:p.(=)
- Pathogenicity Data:
- Best Score: 0.768
- Polyphen2: 0.001 (B)
- SIFT: 0.232 (T)
- Frequency Data:
- TOPMed: 0.0011%
- Phenotypic similarity 0.763 to mouse mutant involving IGF2R.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000562, polydactyly
- HP:0001363, Craniosynostosis - MP:0003416, premature bone ossification
- HP:0011304, Broad thumb - MP:0000562, polydactyly
- HP:0010055, Broad hallux - MP:0000562, polydactyly
- Proximity score 0.501 in interactome to GNAS and phenotypic similarity 0.784 to Pseudohypoparathyroidism type 1A associated with GNAS.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0002684, Thickened calvaria
- HP:0011304, Broad thumb - HP:0009642, Broad distal phalanx of the thumb
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Proximity score 0.501 in interactome to GNAS and phenotypic similarity 0.497 to mouse mutant of GNAS.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0003109, short femur
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb - MP:0003109, short femur
- HP:0010055, Broad hallux - MP:0003109, short femur
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:114550 Hepatocellular carcinoma, somatic - somatic
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.002
Phenotype Score: 0.382
Variant Score: 0.332
- Transcripts:
- IGF2R:ENST00000356956.1:c.3944G>A:p.(Gly1315Glu)
- Pathogenicity Data:
- Best Score: 0.985
- Polyphen2: 0.867 (P)
- SIFT: 0.015 (D)
- Frequency Data:
- 1000Genomes: 0.2396%
- TOPMed: 0.0996%
- ExAC AMR: 0.0086%
- ExAC EAS: 1.3982%
- ExAC NFE: 0.0015%
- ExAC OTH: 0.1101%
- gnomAD_E_AMR: 0.0089%
- gnomAD_E_EAS: 1.4263%
- gnomAD_E_NFE: 0.0045%
- gnomAD_E_OTH: 0.0912%
- gnomAD_G_EAS: 0.9864%
- gnomAD_G_NFE: 0.0133%
- gnomAD_G_OTH: 0.1018%
- Transcripts:
- IGF2R:ENST00000356956.1:c.1218G>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0015%
- ESP AA: 0.0227%
- ESP All: 0.0077%
- ExAC AFR: 0.0096%
- ExAC NFE: 0.0015%
- gnomAD_E_AFR: 0.0065%
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.382
Variant Score: 0.100
- Transcripts:
- IGF2R:ENST00000356956.1:c.1218G>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0015%
- ESP AA: 0.0227%
- ESP All: 0.0077%
- ExAC AFR: 0.0096%
- ExAC NFE: 0.0015%
- gnomAD_E_AFR: 0.0065%
- Transcripts:
- IGF2R:ENST00000356956.1:c.3519C>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0599%
- TOPMed: 0.0268%
- ESP EA: 0.0233%
- ESP All: 0.0154%
- ExAC EAS: 0.4622%
- ExAC NFE: 0.0225%
- gnomAD_E_EAS: 0.5044%
- gnomAD_E_NFE: 0.0170%
- gnomAD_E_OTH: 0.0182%
- gnomAD_E_SAS: 0.0032%
- gnomAD_G_AFR: 0.0114%
- gnomAD_G_EAS: 0.3083%
- gnomAD_G_NFE: 0.0400%
- Phenotypic similarity 0.541 to X-linked non-syndromic intellectual disability associated with ALG13.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0004691, 2-3 toe syndactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0006118, Shortening of all distal phalanges of the fingers
- HP:0010055, Broad hallux - HP:0004691, 2-3 toe syndactyly
- Phenotypic similarity 0.318 to mouse mutant involving ALG13.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Known diseases:
- OMIM:300884 ?Congenital disorder of glycosylation, type Is (unconfirmed)
- OMIM:300884 Developmental and epileptic encephalopathy 36 - X-linked dominant
- ORPHA:324422 ALG13-CDG - X-linked dominant
- ORPHA:777 X-linked non-syndromic intellectual disability - X-linked recessive
X_RECESSIVE
Exomiser Score: 0.002
Phenotype Score: 0.541
Variant Score: 0.150
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.541 to ORPHA:777 X-linked non-syndromic intellectual disability
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC AMR: 0.0831%
- ExAC NFE: 0.0401%
- gnomAD_E_AFR: 0.3811%
- gnomAD_E_AMR: 0.1167%
- gnomAD_E_EAS: 0.2426%
- gnomAD_E_FIN: 0.0282%
- gnomAD_E_NFE: 0.1428%
- gnomAD_E_OTH: 0.2959%
- gnomAD_E_SAS: 0.1309%
- gnomAD_G_AFR: 0.8772%
- gnomAD_G_AMR: 0.2179%
- gnomAD_G_EAS: 1.9582%
- gnomAD_G_FIN: 0.4594%
- gnomAD_G_NFE: 0.8895%
- gnomAD_G_OTH: 0.8197%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.002
Phenotype Score: 0.000
Variant Score: 0.760
- Transcripts:
- SERPINA9:ENST00000298845.7:c.535A>T:p.(Met179Leu)
- SERPINA9:ENST00000337425.5:c.835A>T:p.(Met279Leu)
- SERPINA9:ENST00000380365.3:c.781A>T:p.(Met261Leu)
- SERPINA9:ENST00000424550.2:c.388A>T:p.(Met130Leu)
- SERPINA9:ENST00000448305.2:c.541A>T:p.(Met181Leu)
- SERPINA9:ENST00000546329.1:c.727A>T:p.(Met243Leu)
- Pathogenicity Data:
- Best Score: 0.76
- Polyphen2: 0.596 (P)
- SIFT: 0.240 (T)
- Frequency Data:
- TOPMed: 0.0015%
- No phenotype or PPI evidence
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.002
Phenotype Score: 0.000
Variant Score: 0.756
- Pathogenicity Data:
- Best Score: 1.0
- Polyphen2: 0.986 (D)
- Mutation Taster: 1.000 (P)
- SIFT: 0.005 (D)
- Frequency Data:
- TOPMed: 0.0032%
- ExAC EAS: 0.2187%
- gnomAD_E_EAS: 0.0855%
- Pathogenicity Data:
- Best Score: 0.61300004
- Polyphen2: 0.002 (B)
- SIFT: 0.387 (T)
- Frequency Data:
- 1000Genomes: 0.0998%
- TOPMed: 0.0113%
- ESP AA: 0.0227%
- ESP All: 0.0077%
- ExAC AMR: 0.0174%
- ExAC EAS: 0.1391%
- ExAC FIN: 0.0152%
- ExAC NFE: 0.0108%
- ExAC OTH: 0.2398%
- ExAC SAS: 0.6030%
- gnomAD_E_EAS: 0.1051%
- gnomAD_E_FIN: 0.0093%
- gnomAD_E_NFE: 0.0122%
- gnomAD_E_OTH: 0.0572%
- gnomAD_E_SAS: 0.4967%
- gnomAD_G_NFE: 0.0067%
- gnomAD_G_OTH: 0.2045%
- Phenotypic similarity 0.340 to Combined immunodeficiency-enteropathy spectrum associated with TTC7A.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0008404, Nail dystrophy
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0008404, Nail dystrophy
- HP:0010055, Broad hallux - HP:0008404, Nail dystrophy
- Phenotypic similarity 0.667 to mouse mutant involving TTC7A.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000579, abnormal nail morphology
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0000579, abnormal nail morphology
- HP:0010055, Broad hallux - MP:0000579, abnormal nail morphology
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:243150 Gastrointestinal defects and immunodeficiency syndrome - autosomal recessive
- ORPHA:2300 Multiple intestinal atresia - autosomal recessive
- ORPHA:436252 Combined immunodeficiency-enteropathy spectrum - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.334
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0023%
- ExAC EAS: 0.0465%
- ExAC NFE: 0.0030%
- ExAC SAS: 0.0121%
- gnomAD_E_EAS: 0.0464%
- gnomAD_E_NFE: 0.0036%
- gnomAD_E_OTH: 0.0183%
- gnomAD_E_SAS: 0.0065%
- Proximity score 0.500 in interactome to PRKD1 and phenotypic similarity 0.756 to Congenital heart defects and ectodermal dysplasia associated with PRKD1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001159, Syndactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0011304, Broad thumb
- HP:0010055, Broad hallux - HP:0001159, Syndactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.002
Phenotype Score: 0.500
Variant Score: 0.183
- Transcripts:
- AGTRAP:ENST00000314340.5:c.461A>G:p.(Gln154Arg)
- AGTRAP:ENST00000376629.4:c.440A>G:p.(Gln147Arg)
- AGTRAP:ENST00000510878.1:c.355A>G:p.(Lys119Glu)
- AGTRAP:ENST00000376627.2:c.*114A>G:p.(=)
- AGTRAP:ENST00000376637.3:c.*69A>G:p.(=)
- AGTRAP:ENST00000400895.2:c.*114A>G:p.(=)
- AGTRAP:ENST00000452018.2:c.*69A>G:p.(=)
- Pathogenicity Data:
- Best Score: 0.18300003
- Polyphen2: 0.060 (B)
- SIFT: 0.817 (T)
- Frequency Data:
- TOPMed: 0.0004%
- gnomAD_E_EAS: 0.0058%
- No phenotype or PPI evidence
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.002
Phenotype Score: 0.000
Variant Score: 0.747
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AMR: 0.0225%
- gnomAD_E_FIN: 0.8937%
- gnomAD_E_NFE: 0.1165%
- gnomAD_E_SAS: 0.0038%
- gnomAD_G_AFR: 0.0250%
- gnomAD_G_FIN: 0.0309%
- gnomAD_G_NFE: 0.0658%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AMR: 0.0341%
- gnomAD_E_FIN: 0.8713%
- gnomAD_E_NFE: 0.1408%
- gnomAD_E_SAS: 0.0039%
- gnomAD_G_AFR: 0.0238%
- gnomAD_G_FIN: 0.0586%
- gnomAD_G_NFE: 0.0578%
- Phenotypic similarity 0.571 to mouse mutant involving PTH.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0004634, short metacarpal bones
- HP:0001363, Craniosynostosis - MP:0002896, abnormal bone mineralization
- HP:0011304, Broad thumb - MP:0004634, short metacarpal bones
- HP:0010055, Broad hallux - MP:0004635, short metatarsal bones
- Proximity score 0.518 in interactome to MGP and phenotypic similarity 0.623 to Keutel syndrome associated with MGP.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0009778, Short thumb
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009778, Short thumb
- HP:0010055, Broad hallux - HP:0010109, Short hallux
- Proximity score 0.518 in interactome to MGP and phenotypic similarity 0.527 to mouse mutant of MGP.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0003055, abnormal long bone epiphyseal plate morphology
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb - MP:0003055, abnormal long bone epiphyseal plate morphology
- HP:0010055, Broad hallux - MP:0003055, abnormal long bone epiphyseal plate morphology
- Known diseases:
- OMIM:146200 Hypoparathyroidism, familial isolated 1 - autosomal dominant/recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.002
Phenotype Score: 0.571
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0399%
- TOPMed: 0.0004%
- ExAC EAS: 0.0231%
- gnomAD_E_EAS: 0.0232%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.000
Variant Score: 0.724
- Pathogenicity Data:
- Best Score: 0.725
- Polyphen2: 0.582 (P)
- SIFT: 0.275 (T)
- Frequency Data:
- TOPMed: 0.0004%
- ExAC EAS: 0.0116%
- gnomAD_E_EAS: 0.0058%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.000
Variant Score: 0.722
- Transcripts:
- USP17L18:ENST00000504209.1:c.101G>A:p.(Arg34Gln)
- Pathogenicity Data:
- Best Score: 0.722
- Polyphen2: 0.258 (B)
- SIFT: 0.278 (T)
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.000
Variant Score: 0.694
- Pathogenicity Data:
- Best Score: 0.7
- Polyphen2: 0.035 (B)
- SIFT: 0.300 (T)
- Frequency Data:
- TOPMed: 0.0004%
- ExAC EAS: 0.0231%
- gnomAD_E_EAS: 0.0233%
- gnomAD_G_EAS: 0.0617%
- Proximity score 0.520 in interactome to ZIC1 and phenotypic similarity 0.698 to Isolated brachycephaly associated with ZIC1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0000248, Brachycephaly
- HP:0011304, Broad thumb - HP:0009701, Metacarpal synostosis
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.520
Variant Score: 0.100
- Transcripts:
- EN2:ENST00000297375.4:c.402A>G:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
- gnomAD_G_NFE: 0.0067%
- Proximity score 0.501 in interactome to NEPRO and phenotypic similarity 0.710 to Anauxetic dysplasia 3 associated with NEPRO.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0001357, Plagiocephaly
- HP:0011304, Broad thumb - HP:0009844, Broad middle phalanx of finger
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.501
Variant Score: 0.117
- Pathogenicity Data:
- Best Score: 0.116999984
- Polyphen2: 0.010 (B)
- SIFT: 0.883 (T)
- Frequency Data:
- TOPMed: 0.0042%
- gnomAD_E_AFR: 0.0065%
- gnomAD_E_NFE: 0.0009%
- gnomAD_G_NFE: 0.0067%
- Proximity score 0.516 in interactome to ASPH and phenotypic similarity 0.737 to mouse mutant of ASPH.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000564, syndactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0000564, syndactyly
- HP:0010055, Broad hallux - MP:0000564, syndactyly
- Known diseases:
- OMIM:115000 Ventricular arrythmias due to cardiac ryanodine receptor calcium release deficiency syndrome - autosomal dominant
- OMIM:600996 Arrhythmogenic right ventricular dysplasia 2 - autosomal dominant
- OMIM:604772 Ventricular tachycardia, catecholaminergic polymorphic, 1 - autosomal dominant
- ORPHA:3286 Catecholaminergic polymorphic ventricular tachycardia - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.516
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0015%
- gnomAD_E_EAS: 0.0232%
- Phenotypic similarity 0.427 to Familial thoracic aortic aneurysm and aortic dissection associated with FOXE3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001166, Arachnodactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001166, Arachnodactyly
- HP:0010055, Broad hallux - HP:0001166, Arachnodactyly
- Phenotypic similarity 0.376 to mouse mutant involving FOXE3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0005545, abnormal lens development
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.514 in interactome to ZEB2 and phenotypic similarity 0.818 to Mowat-Wilson syndrome due to monosomy 2q22 associated with ZEB2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010055, Broad hallux
- HP:0001363, Craniosynostosis - HP:0011317, Right unicoronal synostosis
- HP:0011304, Broad thumb - HP:0001181, Adducted thumb
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
- Known diseases:
- OMIM:610256 Anterior segment dysgenesis 2, multiple subtypes - autosomal recessive
- OMIM:617349 Aortic aneurysm, familial thoracic 11, susceptibility to (susceptibility)
- ORPHA:708 Peters anomaly - autosomal dominant/recessive
- ORPHA:83461 Congenital primary aphakia - autosomal recessive
- ORPHA:91387 Familial thoracic aortic aneurysm and aortic dissection - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.514
Variant Score: 0.100
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.427 to ORPHA:91387 Familial thoracic aortic aneurysm and aortic dissection
- Transcripts:
- FOXE3:ENST00000335071.2:c.549G>C:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.484 to mouse mutant involving TP73.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0000440, domed cranium
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.511 in interactome to IFT57 and phenotypic similarity 0.652 to ?Orofaciodigital syndrome XVIII associated with IFT57.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0005819, Short middle phalanx of finger
- HP:0010055, Broad hallux - HP:0001852, Sandal gap
- Proximity score 0.511 in interactome to IFT57 and phenotypic similarity 0.732 to mouse mutant of IFT57.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000562, polydactyly
- HP:0001363, Craniosynostosis - MP:0006197, ocular hypotelorism
- HP:0011304, Broad thumb - MP:0000562, polydactyly
- HP:0010055, Broad hallux - MP:0000562, polydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.511
Variant Score: 0.099
- Transcripts:
- TP73:ENST00000346387.4:c.234C>T:p.(=)
- TP73:ENST00000354437.4:c.234C>T:p.(=)
- TP73:ENST00000357733.3:c.234C>T:p.(=)
- TP73:ENST00000378280.1:c.87C>T:p.(=)
- TP73:ENST00000378285.1:c.87C>T:p.(=)
- TP73:ENST00000378288.4:c.87C>T:p.(=)
- TP73:ENST00000378290.4:c.21C>T:p.(=)
- TP73:ENST00000378295.4:c.234C>T:p.(=)
- TP73:ENST00000603362.1:c.234C>T:p.(=)
- TP73:ENST00000604074.1:c.234C>T:p.(=)
- TP73:ENST00000604479.1:c.234C>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0034%
- ExAC EAS: 0.0466%
- ExAC SAS: 0.0488%
- gnomAD_E_EAS: 0.0754%
- gnomAD_E_SAS: 0.0455%
- gnomAD_G_EAS: 0.0617%
- Proximity score 0.511 in interactome to KIF22 and phenotypic similarity 0.657 to Spondyloepimetaphyseal dysplasia with joint laxity, type 2 associated with KIF22.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0012296, Slender distal phalanx of finger
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009836, Broad distal phalanx of finger
- HP:0010055, Broad hallux - HP:0012296, Slender distal phalanx of finger
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.511
Variant Score: 0.099
- Transcripts:
- KIF4B:ENST00000435029.4:c.3444C>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0079%
- ExAC EAS: 0.0347%
- ExAC NFE: 0.0030%
- gnomAD_E_AFR: 0.0065%
- gnomAD_E_EAS: 0.0870%
- gnomAD_E_NFE: 0.0018%
- gnomAD_E_SAS: 0.0032%
- gnomAD_G_NFE: 0.0067%
- Proximity score 0.510 in interactome to HS6ST1 and phenotypic similarity 0.332 to Hypogonadotropic hypogonadism 15 with or without anosmia associated with HS6ST1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0002857, Genu valgum
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0002857, Genu valgum
- HP:0010055, Broad hallux - HP:0002857, Genu valgum
- Proximity score 0.510 in interactome to HS6ST1 and phenotypic similarity 0.783 to mouse mutant of HS6ST1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0005306, abnormal phalanx morphology
- HP:0001363, Craniosynostosis - MP:0002092, abnormal eye morphology
- HP:0011304, Broad thumb - MP:0005306, abnormal phalanx morphology
- HP:0010055, Broad hallux - MP:0005104, abnormal tarsal bone morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.510
Variant Score: 0.100
- Transcripts:
- GPC5:ENST00000377067.3:c.312G>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0004%
- gnomAD_E_EAS: 0.0058%
- gnomAD_E_NFE: 0.0018%
- gnomAD_E_SAS: 0.0033%
- Proximity score 0.508 in interactome to GRHL2 and phenotypic similarity 0.347 to Ectodermal dysplasia/short stature syndrome associated with GRHL2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0008404, Nail dystrophy
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0008404, Nail dystrophy
- HP:0010055, Broad hallux - HP:0008404, Nail dystrophy
- Proximity score 0.508 in interactome to GRHL2 and phenotypic similarity 0.756 to mouse mutant of GRHL2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000564, syndactyly
- HP:0001363, Craniosynostosis - MP:0011495, abnormal head shape
- HP:0011304, Broad thumb - MP:0000564, syndactyly
- HP:0010055, Broad hallux - MP:0000564, syndactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.508
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0399%
- TOPMed: 0.0060%
- ExAC AMR: 0.0086%
- ExAC EAS: 0.0116%
- ExAC NFE: 0.0015%
- ExAC SAS: 0.0363%
- gnomAD_E_AMR: 0.0089%
- gnomAD_E_EAS: 0.0058%
- gnomAD_E_NFE: 0.0018%
- gnomAD_E_SAS: 0.0227%
- gnomAD_G_NFE: 0.0067%
- Proximity score 0.507 in interactome to KCNJ2 and phenotypic similarity 0.651 to Andersen syndrome associated with KCNJ2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009803, Short phalanx of finger
- HP:0010055, Broad hallux - HP:0001770, Toe syndactyly
- Proximity score 0.507 in interactome to KCNJ2 and phenotypic similarity 0.254 to mouse mutant of KCNJ2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0030248, narrow maxilla
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Known diseases:
- OMIM:609620 Short QT syndrome 1 - autosomal dominant
- OMIM:613688 Long QT syndrome 2 - autosomal dominant
- OMIM:613688 Long QT syndrome 2, acquired, susceptibility to (susceptibility)
- ORPHA:101016 Romano-Ward syndrome - autosomal dominant
- ORPHA:51083 Familial short QT syndrome - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.507
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0015%
- ExAC EAS: 0.0116%
- gnomAD_E_EAS: 0.0174%
- gnomAD_E_NFE: 0.0009%
- Proximity score 0.506 in interactome to TNRC6B and phenotypic similarity 0.869 to Non-specific syndromic intellectual disability associated with TNRC6B.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010109, Short hallux
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0011304, Broad thumb
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.506
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.506 in interactome to SLC35A2 and phenotypic similarity 0.712 to SLC35A2-CDG associated with SLC35A2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001840, Metatarsus adductus
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0100490, Camptodactyly of finger
- HP:0010055, Broad hallux - HP:0001840, Metatarsus adductus
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.506
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0096%
- ESP AA: 0.0454%
- ESP All: 0.0154%
- gnomAD_E_NFE: 0.0018%
- gnomAD_E_SAS: 0.0065%
- gnomAD_G_NFE: 0.0067%
- Phenotypic similarity 0.399 to mouse mutant involving SEPTIN5.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002764, short tibia
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002764, short tibia
- HP:0010055, Broad hallux - MP:0002764, short tibia
- Proximity score 0.506 in interactome to GP1BB and phenotypic similarity 0.740 to 22q11.2 deletion syndrome associated with GP1BB.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001829, Foot polydactyly
- HP:0001363, Craniosynostosis - HP:0011324, Multiple suture craniosynostosis
- HP:0011304, Broad thumb - HP:0001161, Hand polydactyly
- HP:0010055, Broad hallux - HP:0001829, Foot polydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.506
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0032%
- ExAC AMR: 0.0260%
- ExAC NFE: 0.0015%
- gnomAD_E_AMR: 0.0417%
- gnomAD_E_EAS: 0.0116%
- gnomAD_E_NFE: 0.0009%
- Proximity score 0.506 in interactome to NSUN2 and phenotypic similarity 0.810 to Dubowitz syndrome associated with NSUN2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0011304, Broad thumb
- HP:0010055, Broad hallux - HP:0001770, Toe syndactyly
- Proximity score 0.506 in interactome to NSUN2 and phenotypic similarity 0.571 to mouse mutant of NSUN2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0005296, abnormal humerus morphology
- HP:0001363, Craniosynostosis - MP:0002932, abnormal joint morphology
- HP:0011304, Broad thumb - MP:0005296, abnormal humerus morphology
- HP:0010055, Broad hallux - MP:0005296, abnormal humerus morphology
- Known diseases:
- OMIM:614153 Spinocerebellar ataxia 36 - autosomal dominant
- ORPHA:276198 Spinocerebellar ataxia type 36 - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.506
Variant Score: 0.099
- Transcripts:
- NOP56:ENST00000329276.5:c.594G>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0024%
- ExAC SAS: 0.0121%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_SAS: 0.0195%
- gnomAD_G_AFR: 0.0115%
- gnomAD_G_EAS: 0.0617%
- Proximity score 0.505 in interactome to KCNH1 and phenotypic similarity 0.856 to Temple-Baraitser syndrome associated with KCNH1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010055, Broad hallux
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0011304, Broad thumb
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.505
Variant Score: 0.100
- Transcripts:
- KCNA7:ENST00000221444.1:c.333C>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0024%
- Phenotypic similarity 0.483 to mouse mutant involving ULK4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0000440, domed cranium
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.505 in interactome to SUFU and phenotypic similarity 0.657 to Gorlin syndrome associated with SUFU.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0000248, Brachycephaly
- HP:0011304, Broad thumb - HP:0001166, Arachnodactyly
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Proximity score 0.505 in interactome to SUFU and phenotypic similarity 0.722 to mouse mutant of SUFU.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000562, polydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0000562, polydactyly
- HP:0010055, Broad hallux - MP:0000562, polydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.505
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0004%
- ExAC SAS: 0.0061%
- gnomAD_E_SAS: 0.0130%
- Proximity score 0.505 in interactome to STAMBP and phenotypic similarity 0.666 to Microcephaly-capillary malformation syndrome associated with STAMBP.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009882, Short distal phalanx of finger
- HP:0010055, Broad hallux - HP:0030084, Clinodactyly
- Proximity score 0.505 in interactome to STAMBP and phenotypic similarity 0.268 to mouse mutant of STAMBP.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001344, blepharoptosis
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.505
Variant Score: 0.100
- Transcripts:
- RNF11:ENST00000242719.3:c.57T>C:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0056%
- ESP EA: 0.0116%
- ESP All: 0.0077%
- ExAC EAS: 0.0118%
- ExAC NFE: 0.0015%
- gnomAD_E_EAS: 0.0233%
- gnomAD_E_NFE: 0.0009%
- Proximity score 0.504 in interactome to FLNA and phenotypic similarity 0.812 to ?FG syndrome 2 associated with FLNA.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010055, Broad hallux
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0010055, Broad hallux
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
- Proximity score 0.504 in interactome to FLNA and phenotypic similarity 0.583 to mouse mutant of FLNA.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000157, abnormal sternum morphology
- HP:0001363, Craniosynostosis - MP:0001319, irregularly shaped pupil
- HP:0011304, Broad thumb - MP:0000157, abnormal sternum morphology
- HP:0010055, Broad hallux - MP:0000157, abnormal sternum morphology
X_RECESSIVE
Exomiser Score: 0.001
Phenotype Score: 0.504
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0019%
- gnomAD_E_EAS: 0.0079%
X_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.504
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0019%
- gnomAD_E_EAS: 0.0079%
- Phenotypic similarity 0.303 to mouse mutant involving IKBKB.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.504 in interactome to TWIST1 and phenotypic similarity 0.871 to Robinow-Sorauf syndrome associated with TWIST1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010055, Broad hallux
- HP:0001363, Craniosynostosis - HP:0001357, Plagiocephaly
- HP:0011304, Broad thumb - HP:0010055, Broad hallux
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
- Proximity score 0.504 in interactome to TWIST1 and phenotypic similarity 1.000 to mouse mutant of TWIST1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000562, polydactyly
- HP:0001363, Craniosynostosis - MP:0000081, premature cranial suture closure
- HP:0011304, Broad thumb - MP:0000562, polydactyly
- HP:0010055, Broad hallux - MP:0000562, polydactyly
- Known diseases:
- OMIM:615592 Immunodeficiency 15B - autosomal recessive
- OMIM:618204 Immunodeficiency 15A - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.504
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.503 in interactome to PIAS2 and phenotypic similarity 0.727 to mouse mutant of PIAS2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis - MP:0001325, abnormal retina morphology
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.503
Variant Score: 0.100
- Transcripts:
- SEPTIN14:ENST00000388975.3:c.654T>C:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.307 to mouse mutant involving MYO1C.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0000062, increased bone mineral density
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.504 in interactome to EXOC8 and phenotypic similarity 0.635 to ?Neurodevelopmental disorder with microcephaly, seizures, and brain atrophy associated with EXOC8.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.504
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0045%
- ExAC EAS: 0.0924%
- gnomAD_E_EAS: 0.0928%
- gnomAD_G_EAS: 0.0617%
- Proximity score 0.503 in interactome to ACAN and phenotypic similarity 0.885 to Short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans associated with ACAN.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0002007, Frontal bossing
- HP:0011304, Broad thumb - HP:0009778, Short thumb
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
- Proximity score 0.503 in interactome to ACAN and phenotypic similarity 0.853 to mouse mutant of ACAN.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002544, brachydactyly
- HP:0001363, Craniosynostosis - MP:0030420, short basicranium
- HP:0011304, Broad thumb - MP:0002544, brachydactyly
- HP:0010055, Broad hallux - MP:0002544, brachydactyly
- Known diseases:
- OMIM:611543 Cavitary optic disc anomalies - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.503
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Phenotypic similarity 0.318 to mouse mutant involving SMN2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.502 in interactome to SNRPN and phenotypic similarity 0.664 to Prader-Willi syndrome due to translocation associated with SNRPN.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0005469, Flat occiput
- HP:0011304, Broad thumb - HP:0004209, Clinodactyly of the 5th finger
- HP:0010055, Broad hallux - HP:0001845, Overlapping toe
- Known diseases:
- OMIM:253300 Spinal muscular atrophy-1 - autosomal recessive
- OMIM:253400 Spinal muscular atrophy-3 - autosomal recessive
- OMIM:253550 Spinal muscular atrophy-2 - autosomal recessive
- OMIM:271150 Spinal muscular atrophy-4 - autosomal recessive
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.001
Phenotype Score: 0.502
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.251
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.502 in interactome to FGD1 and phenotypic similarity 0.621 to Mental retardation, X-linked syndromic 16 associated with FGD1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009466, Radial deviation of finger
- HP:0010055, Broad hallux - HP:0030084, Clinodactyly
- Proximity score 0.502 in interactome to FGD1 and phenotypic similarity 0.272 to mouse mutant of FGD1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001297, microphthalmia
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.502
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0015%
- ExAC AMR: 0.0091%
- ExAC EAS: 0.0118%
- ExAC SAS: 0.0071%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_EAS: 0.0116%
- gnomAD_E_NFE: 0.0018%
- gnomAD_E_SAS: 0.0066%
- gnomAD_G_NFE: 0.0067%
- Proximity score 0.502 in interactome to RBPJ and phenotypic similarity 0.662 to Adams-Oliver syndrome associated with RBPJ.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0001362, Calvarial skull defect
- HP:0011304, Broad thumb - HP:0009882, Short distal phalanx of finger
- HP:0010055, Broad hallux - HP:0010760, Absent toe
- Proximity score 0.502 in interactome to RBPJ and phenotypic similarity 0.245 to mouse mutant of RBPJ.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0010124, decreased bone mineral content
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.502
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_FIN: 0.0081%
- gnomAD_E_NFE: 0.0063%
- Phenotypic similarity 0.313 to Tuberous sclerosis-1 associated with TSC1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0009724, Subungual fibromas
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009724, Subungual fibromas
- HP:0010055, Broad hallux - HP:0009724, Subungual fibromas
- Proximity score 0.502 in interactome to SFN and phenotypic similarity 0.710 to mouse mutant of SFN.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0005306, abnormal phalanx morphology
- HP:0001363, Craniosynostosis - MP:0000454, abnormal jaw morphology
- HP:0011304, Broad thumb - MP:0005306, abnormal phalanx morphology
- HP:0010055, Broad hallux - MP:0005306, abnormal phalanx morphology
- Known diseases:
- OMIM:191100 Tuberous sclerosis-1 - autosomal dominant
- OMIM:606690 Lymphangioleiomyomatosis - somatic
- OMIM:607341 Focal cortical dysplasia, type II, somatic - somatic
- ORPHA:538 Lymphangioleiomyomatosis (unconfirmed)
- ORPHA:805 Tuberous sclerosis complex - autosomal dominant
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.502
Variant Score: 0.100
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.313 to OMIM:191100 Tuberous sclerosis-1
- Phenotypic similarity 0.296 to ORPHA:805 Tuberous sclerosis complex
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0026%
- ExAC NFE: 0.0030%
- gnomAD_E_NFE: 0.0018%
- gnomAD_E_OTH: 0.0182%
- gnomAD_G_AFR: 0.0115%
- Proximity score 0.502 in interactome to PSMD12 and phenotypic similarity 0.869 to Non-specific syndromic intellectual disability associated with PSMD12.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010109, Short hallux
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0011304, Broad thumb
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.502
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0015%
- gnomAD_E_NFE: 0.0010%
- Phenotypic similarity 0.271 to mouse mutant involving EMX1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0003795, abnormal bone structure
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.501 in interactome to FGF8 and phenotypic similarity 0.681 to Holoprosencephaly associated with FGF8.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0005469, Flat occiput
- HP:0011304, Broad thumb - HP:0001161, Hand polydactyly
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Proximity score 0.501 in interactome to FGF8 and phenotypic similarity 0.737 to mouse mutant of FGF8.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000564, syndactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0000564, syndactyly
- HP:0010055, Broad hallux - MP:0000564, syndactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.501
Variant Score: 0.100
- Transcripts:
- EMX1:ENST00000258106.6:c.550C>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.502 in interactome to HDAC4 and phenotypic similarity 0.656 to 2q37 microdeletion syndrome associated with HDAC4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0002007, Frontal bossing
- HP:0011304, Broad thumb - HP:0006101, Finger syndactyly
- HP:0010055, Broad hallux - HP:0001770, Toe syndactyly
- Proximity score 0.502 in interactome to HDAC4 and phenotypic similarity 0.934 to mouse mutant of HDAC4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000165, abnormal long bone hypertrophic chondrocyte zone
- HP:0001363, Craniosynostosis - MP:0030356, premature lambdoid suture closure
- HP:0011304, Broad thumb - MP:0000165, abnormal long bone hypertrophic chondrocyte zone
- HP:0010055, Broad hallux - MP:0000165, abnormal long bone hypertrophic chondrocyte zone
- Proximity score 0.502 in interactome to HDAC4 and phenotypic similarity 0.614 to fish mutant of HDAC4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - ZP:0107238, anguloarticular premature ossification, abnormal
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.502
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0083%
- gnomAD_E_AFR: 0.0394%
- gnomAD_E_AMR: 0.0030%
- gnomAD_G_AFR: 0.0114%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.001
Phenotype Score: 0.502
Variant Score: 0.087
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0083%
- gnomAD_E_AFR: 0.0394%
- gnomAD_E_AMR: 0.0030%
- gnomAD_G_AFR: 0.0114%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.2995%
- TOPMed: 0.2102%
- ESP AA: 0.4085%
- ESP EA: 0.0233%
- ESP All: 0.1538%
- ExAC AFR: 0.4792%
- ExAC AMR: 0.0266%
- ExAC EAS: 1.0328%
- ExAC NFE: 0.0062%
- gnomAD_E_AFR: 0.3846%
- gnomAD_E_AMR: 0.0229%
- gnomAD_E_EAS: 0.8937%
- gnomAD_E_NFE: 0.0046%
- gnomAD_E_OTH: 0.0569%
- gnomAD_E_SAS: 0.0070%
- gnomAD_G_AFR: 0.3091%
- gnomAD_G_EAS: 0.1850%
- Proximity score 0.501 in interactome to CASP3 and phenotypic similarity 0.631 to mouse mutant of CASP3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0003843, abnormal sagittal suture morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.501
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
- Phenotypic similarity 0.435 to mouse mutant involving IQSEC3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002764, short tibia
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb - MP:0002764, short tibia
- HP:0010055, Broad hallux - MP:0002764, short tibia
- Proximity score 0.501 in interactome to IQSEC2 and phenotypic similarity 0.701 to Smith-Magenis syndrome associated with IQSEC2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0000248, Brachycephaly
- HP:0011304, Broad thumb - HP:0001161, Hand polydactyly
- HP:0010055, Broad hallux - HP:0001770, Toe syndactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.501
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.501 in interactome to CHD4 and phenotypic similarity 0.639 to Sifrim-Hitz-Weiss syndrome associated with CHD4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001182, Tapered finger
- HP:0001363, Craniosynostosis - HP:0002645, Wormian bones
- HP:0011304, Broad thumb - HP:0001182, Tapered finger
- HP:0010055, Broad hallux - HP:0001182, Tapered finger
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.501
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC AMR: 0.0087%
- ExAC EAS: 0.0463%
- ExAC NFE: 0.0015%
- gnomAD_E_EAS: 0.0174%
- gnomAD_E_NFE: 0.0018%
- gnomAD_E_OTH: 0.0183%
- Proximity score 0.501 in interactome to PPP2R1A and phenotypic similarity 0.847 to Mental retardation, autosomal dominant 36 associated with PPP2R1A.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010055, Broad hallux
- HP:0001363, Craniosynostosis - HP:0005487, Prominent metopic ridge
- HP:0011304, Broad thumb - HP:0009179, Deviation of the 5th finger
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.501
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.501 in interactome to LRP4 and phenotypic similarity 0.561 to Cenani-Lenz syndrome associated with LRP4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0009778, Short thumb
- HP:0001363, Craniosynostosis - HP:0002007, Frontal bossing
- HP:0011304, Broad thumb - HP:0009778, Short thumb
- HP:0010055, Broad hallux - HP:0001770, Toe syndactyly
- Proximity score 0.501 in interactome to LRP4 and phenotypic similarity 0.953 to mouse mutant of LRP4.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002544, brachydactyly
- HP:0001363, Craniosynostosis - MP:0008730, fused phalanges
- HP:0011304, Broad thumb - MP:0008730, fused phalanges
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.501
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0011%
- Proximity score 0.500 in interactome to NOTCH1 and phenotypic similarity 0.662 to Adams-Oliver syndrome associated with NOTCH1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0001362, Calvarial skull defect
- HP:0011304, Broad thumb - HP:0009882, Short distal phalanx of finger
- HP:0010055, Broad hallux - HP:0010760, Absent toe
- Proximity score 0.500 in interactome to NOTCH1 and phenotypic similarity 0.254 to mouse mutant of NOTCH1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0010097, abnormal retinal blood vessel morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.500
Variant Score: 0.100
- Transcripts:
- PLEKHG4B:ENST00000283426.6:c.477G>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.500 in interactome to AIM2 and phenotypic similarity 0.755 to mouse mutant of AIM2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.500
Variant Score: 0.100
- Transcripts:
- NOD1:ENST00000222823.4:c.2067G>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0015%
- ExAC NFE: 0.0030%
- gnomAD_E_NFE: 0.0027%
- Proximity score 0.500 in interactome to PUF60 and phenotypic similarity 0.818 to Intellectual disability-cardiac anomalies-short stature-joint laxity syndrome associated with PUF60.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0009237, Short 5th finger
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0011304, Broad thumb
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.500
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0004%
- Proximity score 0.500 in interactome to NEPRO and phenotypic similarity 0.710 to Anauxetic dysplasia 3 associated with NEPRO.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0001357, Plagiocephaly
- HP:0011304, Broad thumb - HP:0009844, Broad middle phalanx of finger
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.500
Variant Score: 0.100
- Transcripts:
- FBXO39:ENST00000321535.4:c.91C>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.500 in interactome to L1CAM and phenotypic similarity 0.481 to Hydrocephalus with congenital idiopathic intestinal pseudoobstruction associated with L1CAM.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001181, Adducted thumb
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001181, Adducted thumb
- HP:0010055, Broad hallux - HP:0001181, Adducted thumb
- Proximity score 0.500 in interactome to L1CAM and phenotypic similarity 0.675 to mouse mutant of L1CAM.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000583, long toenails
- HP:0001363, Craniosynostosis - MP:0006198, enophthalmos
- HP:0011304, Broad thumb - MP:0000583, long toenails
- HP:0010055, Broad hallux - MP:0000583, long toenails
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.001
Phenotype Score: 0.500
Variant Score: 0.100
- Transcripts:
- RIMBP3:ENST00000426804.1:c.4530C>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Proximity score 0.501 in interactome to SOX14 and phenotypic similarity 0.755 to mouse mutant of SOX14.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.501
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0242%
- UK10K: 0.0264%
- ESP AA: 0.0227%
- ESP EA: 0.0116%
- ESP All: 0.0154%
- ExAC AFR: 0.0096%
- ExAC AMR: 0.0173%
- ExAC NFE: 0.0317%
- ExAC SAS: 0.0065%
- gnomAD_E_AFR: 0.0066%
- gnomAD_E_AMR: 0.0331%
- gnomAD_E_NFE: 0.0441%
- gnomAD_E_SAS: 0.0033%
- gnomAD_G_NFE: 0.0400%
- Proximity score 0.500 in interactome to FIBP and phenotypic similarity 0.656 to Tall stature-intellectual disability-renal anomalies syndrome associated with FIBP.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001847, Long hallux
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001172, Abnormal thumb morphology
- HP:0010055, Broad hallux - HP:0001847, Long hallux
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.500
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0004%
- ExAC EAS: 0.0116%
- ExAC NFE: 0.0015%
- gnomAD_E_EAS: 0.0117%
- gnomAD_E_NFE: 0.0018%
- Proximity score 0.500 in interactome to TELO2 and phenotypic similarity 0.650 to TELO2-related intellectual disability-neurodevelopmental disorder associated with TELO2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001182, Tapered finger
- HP:0010055, Broad hallux - HP:0004692, 4-5 toe syndactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.500
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_SAS: 0.0032%
- Proximity score 0.500 in interactome to PLOD2 and phenotypic similarity 0.617 to Bruck syndrome 2 associated with PLOD2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0002980, Femoral bowing
- HP:0001363, Craniosynostosis - HP:0002645, Wormian bones
- HP:0011304, Broad thumb - HP:0002980, Femoral bowing
- HP:0010055, Broad hallux - HP:0002980, Femoral bowing
- Proximity score 0.500 in interactome to PLOD2 and phenotypic similarity 0.265 to mouse mutant of PLOD2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0005544, corneal deposits
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.500 in interactome to PLOD2 and phenotypic similarity 0.433 to fish mutant of PLOD2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - ZP:0006781, bone mineralization increased process quality, abnormal
- HP:0011304, Broad thumb - ZP:0020434, rib curved, abnormal
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.500
Variant Score: 0.100
- Transcripts:
- ARL14EP:ENST00000282032.3:c.222A>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
- ExAC EAS: 0.0231%
- gnomAD_E_EAS: 0.0232%
- Proximity score 0.500 in interactome to FBN2 and phenotypic similarity 0.510 to Contractural arachnodactyly, congenital associated with FBN2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001166, Arachnodactyly
- HP:0001363, Craniosynostosis - HP:0000268, Dolichocephaly
- HP:0011304, Broad thumb - HP:0001181, Adducted thumb
- HP:0010055, Broad hallux - HP:0001166, Arachnodactyly
- Proximity score 0.500 in interactome to FBN2 and phenotypic similarity 0.790 to mouse mutant of FBN2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000564, syndactyly
- HP:0001363, Craniosynostosis - MP:0008730, fused phalanges
- HP:0011304, Broad thumb - MP:0008730, fused phalanges
- HP:0010055, Broad hallux - MP:0000564, syndactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.500
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0023%
- ExAC NFE: 0.0106%
- ExAC SAS: 0.0206%
- gnomAD_E_NFE: 0.0047%
- gnomAD_E_SAS: 0.0099%
- gnomAD_G_NFE: 0.0067%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.001
Phenotype Score: 0.500
Variant Score: 0.077
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0023%
- ExAC NFE: 0.0106%
- ExAC SAS: 0.0206%
- gnomAD_E_NFE: 0.0047%
- gnomAD_E_SAS: 0.0099%
- gnomAD_G_NFE: 0.0067%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0599%
- TOPMed: 0.0397%
- ESP EA: 0.0241%
- ESP All: 0.0163%
- ExAC AMR: 0.0362%
- ExAC EAS: 1.4658%
- ExAC NFE: 0.0185%
- gnomAD_E_AMR: 0.0034%
- gnomAD_E_EAS: 1.0591%
- gnomAD_E_NFE: 0.0116%
- gnomAD_E_OTH: 0.0217%
- gnomAD_G_EAS: 0.8631%
- gnomAD_G_NFE: 0.0067%
- Proximity score 0.500 in interactome to RXRA and phenotypic similarity 0.772 to mouse mutant of RXRA.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis - MP:0002092, abnormal eye morphology
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.500
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0048%
- ExAC AMR: 0.0266%
- ExAC EAS: 0.0234%
- gnomAD_E_AMR: 0.0278%
- gnomAD_E_EAS: 0.0118%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_OTH: 0.0187%
- Proximity score 0.500 in interactome to SIAH1 and phenotypic similarity 0.858 to Buratti-Harel syndrome associated with SIAH1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010055, Broad hallux
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0011304, Broad thumb
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.500
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0011%
- ExAC EAS: 0.0347%
- gnomAD_E_EAS: 0.0174%
- Proximity score 0.500 in interactome to TELO2 and phenotypic similarity 0.650 to TELO2-related intellectual disability-neurodevelopmental disorder associated with TELO2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001182, Tapered finger
- HP:0010055, Broad hallux - HP:0004692, 4-5 toe syndactyly
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.500
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0129%
- ESP AA: 0.0227%
- ESP All: 0.0077%
- ExAC AFR: 0.0196%
- ExAC NFE: 0.0031%
- gnomAD_E_AFR: 0.0131%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_NFE: 0.0018%
- gnomAD_E_OTH: 0.0183%
- gnomAD_G_AFR: 0.0458%
- gnomAD_G_NFE: 0.0133%
- Proximity score 0.500 in interactome to FGFR2 and phenotypic similarity 0.880 to Jackson-Weiss syndrome associated with FGFR2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010055, Broad hallux
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0001783, Broad metatarsal
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
- Proximity score 0.500 in interactome to FGFR2 and phenotypic similarity 1.000 to mouse mutant of FGFR2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000157, abnormal sternum morphology
- HP:0001363, Craniosynostosis - MP:0000081, premature cranial suture closure
- HP:0011304, Broad thumb - MP:0000157, abnormal sternum morphology
- HP:0010055, Broad hallux - MP:0000157, abnormal sternum morphology
- Known diseases:
- OMIM:245340 Erythrocyte lactate transporter defect - autosomal dominant
- OMIM:610021 Hyperinsulinemic hypoglycemia, familial, 7 - autosomal dominant
- OMIM:616095 Monocarboxylate transporter 1 deficiency - autosomal dominant/recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.500
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0040%
- ExAC EAS: 0.0347%
- ExAC SAS: 0.0182%
- gnomAD_E_EAS: 0.0348%
- gnomAD_E_SAS: 0.0162%
- gnomAD_G_EAS: 0.0617%
- Proximity score 0.500 in interactome to FIBP and phenotypic similarity 0.656 to Tall stature-intellectual disability-renal anomalies syndrome associated with FIBP.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001847, Long hallux
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001172, Abnormal thumb morphology
- HP:0010055, Broad hallux - HP:0001847, Long hallux
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.500
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0178%
- ESP AA: 0.0908%
- ESP EA: 0.0349%
- ESP All: 0.0538%
- ExAC AFR: 0.0195%
- ExAC AMR: 0.0261%
- ExAC FIN: 0.0303%
- ExAC NFE: 0.0213%
- gnomAD_E_AFR: 0.0131%
- gnomAD_E_AMR: 0.0238%
- gnomAD_E_FIN: 0.0730%
- gnomAD_E_NFE: 0.0199%
- gnomAD_G_AFR: 0.0229%
- gnomAD_G_FIN: 0.0573%
- gnomAD_G_NFE: 0.0267%
- Proximity score 0.500 in interactome to MAPK1 and phenotypic similarity 0.619 to Noonan syndrome 13 associated with MAPK1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0030084, Clinodactyly
- HP:0001363, Craniosynostosis - HP:0005487, Prominent metopic ridge
- HP:0011304, Broad thumb - HP:0001182, Tapered finger
- HP:0010055, Broad hallux - HP:0001845, Overlapping toe
X_RECESSIVE
Exomiser Score: 0.001
Phenotype Score: 0.500
Variant Score: 0.095
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0265%
- TOPMed: 0.0111%
- ExAC EAS: 0.2718%
- ExAC NFE: 0.0021%
- gnomAD_E_EAS: 0.2021%
- gnomAD_E_NFE: 0.0025%
- gnomAD_E_OTH: 0.0494%
- gnomAD_G_EAS: 0.2882%
- gnomAD_G_OTH: 0.1376%
- Phenotypic similarity 0.570 to Hyperphosphatasia-intellectual disability syndrome associated with PGAP3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0030084, Clinodactyly
- HP:0001363, Craniosynostosis - HP:0001357, Plagiocephaly
- HP:0011304, Broad thumb - HP:0006118, Shortening of all distal phalanges of the fingers
- HP:0010055, Broad hallux - HP:0030084, Clinodactyly
- Phenotypic similarity 0.315 to mouse mutant involving PGAP3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002111, abnormal tail morphology
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002111, abnormal tail morphology
- HP:0010055, Broad hallux - MP:0002111, abnormal tail morphology
- Proximity score 0.500 in interactome to MOGS and phenotypic similarity 0.479 to Congenital disorder of glycosylation, type IIb associated with MOGS.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0010557, Overlapping fingers
- HP:0001363, Craniosynostosis - HP:0000269, Prominent occiput
- HP:0011304, Broad thumb - HP:0010557, Overlapping fingers
- HP:0010055, Broad hallux - HP:0010557, Overlapping fingers
- Proximity score 0.500 in interactome to MOGS and phenotypic similarity 0.920 to mouse mutant of MOGS.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002544, brachydactyly
- HP:0001363, Craniosynostosis - MP:0000063, decreased bone mineral density
- HP:0011304, Broad thumb - MP:0002544, brachydactyly
- HP:0010055, Broad hallux - MP:0002544, brachydactyly
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:615716 Hyperphosphatasia with mental retardation syndrome 4 - autosomal recessive
- ORPHA:247262 Hyperphosphatasia-intellectual disability syndrome - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.250
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0068%
- ExAC SAS: 0.0370%
- gnomAD_E_SAS: 0.0171%
- gnomAD_G_EAS: 0.0617%
- Phenotypic similarity 0.346 to mouse mutant involving SLC4A11.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0005301, abnormal corneal endothelium morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.500 in interactome to CCNQ and phenotypic similarity 0.780 to STAR syndrome associated with CCNQ.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001770, Toe syndactyly
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0004209, Clinodactyly of the 5th finger
- HP:0010055, Broad hallux - HP:0001770, Toe syndactyly
- Known diseases:
- OMIM:217400 Corneal endothelial dystrophy and perceptive deafness - autosomal recessive
- OMIM:217700 Corneal endothelial dystrophy, autosomal recessive - autosomal recessive
- OMIM:613268 Corneal dystrophy, Fuchs endothelial, 4 - autosomal dominant
- ORPHA:1490 Corneal dystrophy-perceptive deafness syndrome - autosomal recessive
- ORPHA:293603 Congenital hereditary endothelial dystrophy type II - autosomal recessive
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.001
Phenotype Score: 0.500
Variant Score: 0.077
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.1198%
- TOPMed: 0.1043%
- ExAC AMR: 0.0087%
- ExAC EAS: 0.9024%
- ExAC NFE: 0.0090%
- ExAC SAS: 0.0787%
- gnomAD_E_AMR: 0.0119%
- gnomAD_E_EAS: 0.9508%
- gnomAD_E_NFE: 0.0090%
- gnomAD_E_SAS: 0.0780%
- gnomAD_G_EAS: 0.8631%
- gnomAD_G_NFE: 0.0067%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.1797%
- TOPMed: 0.1311%
- ESP AA: 0.1135%
- ESP All: 0.0384%
- ExAC AFR: 0.1784%
- ExAC AMR: 0.0087%
- ExAC EAS: 0.8958%
- ExAC NFE: 0.0121%
- ExAC OTH: 0.1119%
- ExAC SAS: 0.0730%
- gnomAD_E_AFR: 0.2299%
- gnomAD_E_AMR: 0.0179%
- gnomAD_E_EAS: 1.0214%
- gnomAD_E_NFE: 0.0109%
- gnomAD_E_OTH: 0.0367%
- gnomAD_E_SAS: 0.0845%
- gnomAD_G_AFR: 0.2070%
- gnomAD_G_EAS: 0.9864%
- gnomAD_G_NFE: 0.0067%
- No phenotype or PPI evidence
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:618084 Peeling skin syndrome 6 - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.001
Phenotype Score: 0.000
Variant Score: 0.637
- Transcripts:
- FLG2:ENST00000388718.5:c.5426G>C:p.(Ser1809Thr)
- Pathogenicity Data:
- Best Score: 0.63699996
- Polyphen2: 0.007 (B)
- SIFT: 0.363 (T)
- Frequency Data:
- TOPMed: 0.0008%
- Phenotypic similarity 0.323 to Peeling skin syndrome 1 associated with CDSN.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001806, Onycholysis
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001806, Onycholysis
- HP:0010055, Broad hallux - HP:0001806, Onycholysis
- Phenotypic similarity 0.332 to mouse mutant involving CDSN.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001303, abnormal lens morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Known diseases:
- OMIM:146520 Hypotrichosis 2 - autosomal dominant
- OMIM:270300 Peeling skin syndrome 1 - autosomal recessive
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.000
Phenotype Score: 0.332
Variant Score: 0.237
- Phenotype matches to diseases consistent with this MOI:
- Phenotypic similarity 0.323 to OMIM:270300 Peeling skin syndrome 1
- Pathogenicity Data:
- Best Score: 1.0
- SIFT: 0.000 (D)
- Frequency Data:
- 1000Genomes: 0.5192%
- TOPMed: 0.1058%
- ExAC AFR: 0.0325%
- ExAC AMR: 0.2715%
- ExAC EAS: 1.7176%
- ExAC FIN: 0.1224%
- ExAC NFE: 0.0177%
- ExAC OTH: 0.1144%
- ExAC SAS: 0.0379%
- gnomAD_E_AFR: 0.0282%
- gnomAD_E_AMR: 0.2316%
- gnomAD_E_EAS: 1.4615%
- gnomAD_E_FIN: 0.1096%
- gnomAD_E_NFE: 0.0143%
- gnomAD_E_OTH: 0.0377%
- gnomAD_E_SAS: 0.0304%
- gnomAD_G_AFR: 0.0121%
- gnomAD_G_AMR: 0.2421%
- gnomAD_G_EAS: 1.8916%
- gnomAD_G_FIN: 0.2367%
- Pathogenicity Data:
- Best Score: 0.99
- SIFT: 0.010 (D)
- Frequency Data:
- 1000Genomes: 0.5192%
- TOPMed: 0.1633%
- ESP AA: 0.0227%
- ESP All: 0.0077%
- ExAC AFR: 0.0322%
- ExAC AMR: 0.2714%
- ExAC EAS: 1.7163%
- ExAC FIN: 0.1224%
- ExAC NFE: 0.0176%
- ExAC OTH: 0.1142%
- ExAC SAS: 0.0379%
- gnomAD_E_AFR: 0.0282%
- gnomAD_E_AMR: 0.2320%
- gnomAD_E_EAS: 1.4669%
- gnomAD_E_FIN: 0.1096%
- gnomAD_E_NFE: 0.0143%
- gnomAD_E_OTH: 0.0378%
- gnomAD_E_SAS: 0.0305%
- gnomAD_G_AFR: 0.0121%
- gnomAD_G_AMR: 0.2421%
- gnomAD_G_EAS: 1.8916%
- gnomAD_G_FIN: 0.2365%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.3794%
- TOPMed: 0.0808%
- UK10K: 0.0264%
- ESP AA: 0.1135%
- ESP EA: 0.0465%
- ESP All: 0.0692%
- ExAC AFR: 0.0483%
- ExAC AMR: 0.0432%
- ExAC EAS: 1.3179%
- ExAC NFE: 0.0435%
- ExAC OTH: 0.2208%
- ExAC SAS: 0.0182%
- gnomAD_E_AFR: 0.0458%
- gnomAD_E_AMR: 0.0774%
- gnomAD_E_EAS: 1.1887%
- gnomAD_E_FIN: 0.0090%
- gnomAD_E_NFE: 0.0376%
- gnomAD_E_OTH: 0.1094%
- gnomAD_E_SAS: 0.0292%
- gnomAD_G_AFR: 0.0344%
- gnomAD_G_EAS: 0.2469%
- gnomAD_G_NFE: 0.0334%
- Phenotypic similarity 0.325 to zebrafish mutant involving NDC80.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - ZP:0000399, head flat, abnormal
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.506 in interactome to SMC1A and phenotypic similarity 0.790 to Developmental and epileptic encephalopathy 85, with or without midline brain defects associated with SMC1A.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0030084, Clinodactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0009471, Contracture of the proximal interphalangeal joint of the 3rd finger
- HP:0010055, Broad hallux - HP:0010055, Broad hallux
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.506
Variant Score: 0.029
- Transcripts:
- NDC80:ENST00000261597.4:c.1685G>A:p.(Arg562Gln)
- Pathogenicity Data:
- Best Score: 0.028999984
- Polyphen2: 0.002 (B)
- SIFT: 0.971 (T)
- Frequency Data:
- TOPMed: 0.0008%
- gnomAD_E_AFR: 0.0196%
- gnomAD_E_EAS: 0.0465%
- gnomAD_E_SAS: 0.0195%
- gnomAD_G_EAS: 0.0617%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.600
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.595
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AMR: 0.0102%
- gnomAD_E_EAS: 0.1059%
- gnomAD_E_NFE: 0.0060%
- gnomAD_E_OTH: 0.0722%
- gnomAD_E_SAS: 0.0157%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.600
- Transcripts:
- LINC02897:ENST00000408893.2:c.638G>T:p.(Trp213Leu)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.600
- Transcripts:
- SPATA31A2:ENST00000456183.2:c.1529T>C:p.(Leu510Pro)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.600
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0032%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.600
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0024%
- gnomAD_E_EAS: 0.0058%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.599
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0086%
- gnomAD_E_NFE: 0.0038%
- gnomAD_E_SAS: 0.0043%
- gnomAD_G_AFR: 0.0115%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.598
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0086%
- gnomAD_E_NFE: 0.0038%
- gnomAD_E_SAS: 0.0043%
- gnomAD_G_AFR: 0.0115%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AMR: 0.0061%
- gnomAD_E_NFE: 0.0058%
- gnomAD_G_FIN: 0.0287%
- gnomAD_G_NFE: 0.0133%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AMR: 0.1309%
- gnomAD_E_EAS: 0.0061%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_OTH: 0.0557%
- gnomAD_E_SAS: 0.0034%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.593
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0440%
- gnomAD_E_EAS: 0.0066%
- gnomAD_E_FIN: 0.0804%
- gnomAD_E_NFE: 0.0324%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.593
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0440%
- gnomAD_E_EAS: 0.0066%
- gnomAD_E_FIN: 0.0804%
- gnomAD_E_NFE: 0.0324%
- Transcripts:
- NBPF1:ENST00000430580.2:c.49A>T:p.(Ile17Phe)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0064%
- ExAC EAS: 0.0925%
- ExAC SAS: 0.0061%
- gnomAD_E_EAS: 0.0290%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0871%
- gnomAD_E_AMR: 0.0151%
- gnomAD_E_EAS: 0.3599%
- gnomAD_E_FIN: 0.0094%
- gnomAD_E_NFE: 0.0225%
- gnomAD_E_OTH: 0.0190%
- gnomAD_E_SAS: 0.0427%
- gnomAD_G_AFR: 0.2393%
- gnomAD_G_EAS: 0.5921%
- gnomAD_G_NFE: 0.0745%
- gnomAD_G_OTH: 0.1129%
- Transcripts:
- NBPF1:ENST00000430580.2:c.834T>C:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.1955%
- gnomAD_E_AMR: 0.1293%
- gnomAD_E_EAS: 0.0557%
- gnomAD_E_FIN: 0.1477%
- gnomAD_E_NFE: 0.1257%
- gnomAD_E_OTH: 0.2194%
- gnomAD_E_SAS: 0.0810%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0870%
- gnomAD_E_AMR: 0.0091%
- gnomAD_E_EAS: 0.3785%
- gnomAD_E_FIN: 0.0183%
- gnomAD_E_NFE: 0.0187%
- gnomAD_E_OTH: 0.0568%
- gnomAD_E_SAS: 0.0427%
- gnomAD_G_AFR: 0.2390%
- gnomAD_G_EAS: 0.7864%
- gnomAD_G_NFE: 0.0811%
- gnomAD_G_OTH: 0.1134%
- Proximity score 0.500 in interactome to SCLT1 and phenotypic similarity 0.720 to mouse mutant of SCLT1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0009743, preaxial polydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0009743, preaxial polydactyly
- HP:0010055, Broad hallux - MP:0009743, preaxial polydactyly
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.000
Phenotype Score: 0.500
Variant Score: 0.012
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.5391%
- TOPMed: 0.3321%
- ExAC AFR: 0.5305%
- ExAC AMR: 0.5221%
- ExAC EAS: 1.8813%
- ExAC FIN: 0.1979%
- ExAC NFE: 0.1598%
- ExAC OTH: 1.0090%
- ExAC SAS: 0.2124%
- gnomAD_E_AFR: 0.4915%
- gnomAD_E_AMR: 0.3905%
- gnomAD_E_EAS: 1.8480%
- gnomAD_E_FIN: 0.0901%
- gnomAD_E_NFE: 0.1697%
- gnomAD_E_OTH: 0.4750%
- gnomAD_E_SAS: 0.1885%
- gnomAD_G_AFR: 0.6438%
- gnomAD_G_AMR: 0.1193%
- gnomAD_G_EAS: 1.4180%
- gnomAD_G_FIN: 0.0859%
- gnomAD_G_NFE: 0.1942%
- gnomAD_G_OTH: 0.2045%
- Pathogenicity Data:
- Best Score: 0.0
- Polyphen2: 0.000 (B)
- SIFT: 1.000 (T)
- Frequency Data:
- 1000Genomes: 0.6190%
- TOPMed: 0.3560%
- ESP AA: 0.5901%
- ESP EA: 0.0581%
- ESP All: 0.2384%
- ExAC AFR: 0.4883%
- ExAC AMR: 0.2523%
- ExAC EAS: 1.8817%
- ExAC FIN: 0.0304%
- ExAC NFE: 0.0949%
- ExAC OTH: 0.1116%
- ExAC SAS: 0.1274%
- gnomAD_E_AFR: 0.5501%
- gnomAD_E_AMR: 0.2235%
- gnomAD_E_EAS: 1.8129%
- gnomAD_E_FIN: 0.0090%
- gnomAD_E_NFE: 0.0610%
- gnomAD_E_OTH: 0.2925%
- gnomAD_E_SAS: 0.1008%
- gnomAD_G_AFR: 0.5295%
- gnomAD_G_AMR: 0.3580%
- gnomAD_G_EAS: 1.2963%
- gnomAD_G_FIN: 0.0573%
- gnomAD_G_NFE: 0.0336%
- Phenotypic similarity 0.479 to Autoimmune pulmonary alveolar proteinosis associated with HLA-DRB1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001217, Clubbing
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001217, Clubbing
- HP:0010055, Broad hallux - HP:0001217, Clubbing
- Proximity score 0.504 in interactome to SEC24C and phenotypic similarity 0.740 to 22q11.2 deletion syndrome associated with SEC24C.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001829, Foot polydactyly
- HP:0001363, Craniosynostosis - HP:0011324, Multiple suture craniosynostosis
- HP:0011304, Broad thumb - HP:0001161, Hand polydactyly
- HP:0010055, Broad hallux - HP:0001829, Foot polydactyly
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:126200 Multiple sclerosis, susceptibility to, 1 (susceptibility)
- OMIM:181000 Sarcoidosis, susceptibility to, 1 (susceptibility)
- ORPHA:2073 Narcolepsy type 1 (susceptibility)
- ORPHA:220402 Limited cutaneous systemic sclerosis (susceptibility)
- ORPHA:397 Giant cell arteritis (susceptibility)
- ORPHA:545 Follicular lymphoma (susceptibility)
- ORPHA:747 Autoimmune pulmonary alveolar proteinosis (susceptibility)
- ORPHA:797 Sarcoidosis (susceptibility)
- ORPHA:85414 Systemic-onset juvenile idiopathic arthritis (susceptibility)
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.000
Phenotype Score: 0.252
Variant Score: 0.162
- Transcripts:
- HLA-DRB1:ENST00000360004.5:c.764-6T>C:p.?
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.4631%
- gnomAD_E_AMR: 0.2896%
- gnomAD_E_EAS: 0.8238%
- gnomAD_E_FIN: 0.1160%
- gnomAD_E_NFE: 0.3312%
- gnomAD_E_OTH: 0.3086%
- gnomAD_E_SAS: 0.3272%
- gnomAD_G_AFR: 1.4742%
- gnomAD_G_AMR: 0.6211%
- gnomAD_G_EAS: 1.7271%
- gnomAD_G_FIN: 0.6720%
- gnomAD_G_NFE: 1.5136%
- gnomAD_G_OTH: 1.5000%
- Transcripts:
- HLA-DRB1:ENST00000360004.5:c.399A>C:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.4615%
- gnomAD_E_AMR: 0.3676%
- gnomAD_E_EAS: 0.8338%
- gnomAD_E_FIN: 0.0143%
- gnomAD_E_NFE: 0.2176%
- gnomAD_E_OTH: 0.3798%
- gnomAD_E_SAS: 0.2057%
- gnomAD_G_AFR: 1.2306%
- gnomAD_G_AMR: 0.7062%
- gnomAD_G_EAS: 1.8822%
- gnomAD_G_FIN: 1.0424%
- gnomAD_G_NFE: 1.0781%
- gnomAD_G_OTH: 1.3447%
- Transcripts:
- HLA-DRB1:ENST00000360004.5:c.594G>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_G_AFR: 1.4300%
- gnomAD_G_AMR: 0.9434%
- gnomAD_G_EAS: 1.9203%
- gnomAD_G_FIN: 0.4012%
- gnomAD_G_NFE: 1.4284%
- gnomAD_G_OTH: 0.9346%
- Proximity score 0.501 in interactome to ITGB1BP1 and phenotypic similarity 0.750 to mouse mutant of ITGB1BP1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0004509, abnormal pelvic girdle bone morphology
- HP:0001363, Craniosynostosis - MP:0003840, abnormal coronal suture morphology
- HP:0011304, Broad thumb - MP:0004509, abnormal pelvic girdle bone morphology
- HP:0010055, Broad hallux - MP:0004509, abnormal pelvic girdle bone morphology
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.501
Variant Score: 0.000
- Transcripts:
- HEG1:ENST00000311127.4:c.1063A>G:p.(Lys355Glu)
- Pathogenicity Data:
- Best Score: 0.0
- Polyphen2: 0.000 (B)
- SIFT: 1.000 (T)
- Frequency Data:
- TOPMed: 0.0038%
- ExAC AMR: 0.0088%
- ExAC EAS: 0.0117%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_EAS: 0.0522%
- Phenotypic similarity 0.274 to Autosomal recessive spastic paraplegia type 74 associated with IBA57.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux - HP:0001761, Pes cavus
- Proximity score 0.500 in interactome to NUBP1 and phenotypic similarity 0.794 to mouse mutant of NUBP1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis - MP:0001304, cataract
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:615330 Multiple mitochondrial dysfunctions syndrome 3 - autosomal recessive
- OMIM:616451 ?Spastic paraplegia 74, autosomal recessive (unconfirmed)
- ORPHA:468661 Autosomal recessive spastic paraplegia type 74 - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.250
Variant Score: 0.278
- Pathogenicity Data:
- Best Score: 0.278
- Polyphen2: 0.022 (B)
- SIFT: 0.722 (T)
- Frequency Data:
- ExAC NFE: 0.0031%
- gnomAD_E_NFE: 0.0027%
- Phenotypic similarity 0.479 to Surfactant metabolism dysfunction, pulmonary, 3 associated with ABCA3.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001217, Clubbing
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0001217, Clubbing
- HP:0010055, Broad hallux - HP:0001217, Clubbing
- Proximity score 0.500 in interactome to ETV5 and phenotypic similarity 0.737 to mouse mutant of ETV5.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000562, polydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0000562, polydactyly
- HP:0010055, Broad hallux - MP:0000562, polydactyly
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:610921 Surfactant metabolism dysfunction, pulmonary, 3 - autosomal recessive
- ORPHA:2032 Idiopathic pulmonary fibrosis - polygenic
- ORPHA:70587 Infant acute respiratory distress syndrome - unknown
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.250
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0034%
- ExAC AFR: 0.0096%
- ExAC AMR: 0.0086%
- ExAC EAS: 0.0116%
- ExAC NFE: 0.0090%
- ExAC SAS: 0.0061%
- gnomAD_E_AFR: 0.0131%
- gnomAD_E_EAS: 0.0058%
- gnomAD_E_FIN: 0.0090%
- gnomAD_E_NFE: 0.0045%
- gnomAD_E_SAS: 0.0065%
- No phenotype or PPI evidence
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.538
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AMR: 0.0035%
- gnomAD_E_EAS: 0.0382%
- gnomAD_E_NFE: 0.0047%
- gnomAD_E_OTH: 0.0393%
- gnomAD_G_AFR: 0.1902%
- gnomAD_G_AMR: 0.7163%
- gnomAD_G_EAS: 1.1881%
- gnomAD_G_FIN: 0.7033%
- gnomAD_G_NFE: 0.2903%
- gnomAD_G_OTH: 0.5580%
- Transcripts:
- NPIPA5:ENST00000360151.4:c.940_977del:p.(Thr314fs)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.0072%
- gnomAD_E_AMR: 0.0070%
- gnomAD_E_EAS: 0.0398%
- gnomAD_E_NFE: 0.0028%
- gnomAD_E_OTH: 0.0394%
- gnomAD_G_AFR: 0.2922%
- gnomAD_G_AMR: 0.7862%
- gnomAD_G_EAS: 1.5660%
- gnomAD_G_FIN: 1.0480%
- gnomAD_G_NFE: 0.5083%
- gnomAD_G_OTH: 0.8373%
- No phenotype or PPI evidence
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.521
- Transcripts:
- PCDHA8:ENST00000378123.3:c.165G>T:p.(Glu55Asp)
- PCDHA8:ENST00000531613.1:c.165G>T:p.(Glu55Asp)
- PCDHA8:ENST00000527624.1:c.1602+11793G>T:p.(=)
- PCDHA8:ENST00000529310.1:c.2394+11001G>T:p.(=)
- PCDHA8:ENST00000525929.1:c.2355+4748G>T:p.(=)
- PCDHA8:ENST00000529619.1:c.2352+17359G>T:p.(=)
- PCDHA8:ENST00000529859.1:c.2352+17359G>T:p.(=)
- PCDHA8:ENST00000512229.2:c.2385+31914G>T:p.(=)
- PCDHA8:ENST00000530339.1:c.2385+31914G>T:p.(=)
- PCDHA8:ENST00000526136.1:c.2388+44134G>T:p.(=)
- PCDHA8:ENST00000394633.3:c.1602+53594G>T:p.(=)
- PCDHA8:ENST00000504120.2:c.2394+52802G>T:p.(=)
- PCDHA8:ENST00000522353.2:c.2394+37895G>T:p.(=)
- Pathogenicity Data:
- Best Score: 0.999959
- Polyphen2: 0.012 (B)
- Mutation Taster: 1.000 (P)
- SIFT: 0.169 (T)
- Frequency Data:
- gnomAD_E_AFR: 0.0270%
- gnomAD_E_AMR: 0.3382%
- gnomAD_E_EAS: 0.1847%
- gnomAD_E_FIN: 0.0433%
- gnomAD_E_NFE: 0.0789%
- gnomAD_E_OTH: 0.1034%
- gnomAD_E_SAS: 0.0645%
- gnomAD_G_EAS: 0.1312%
- gnomAD_G_FIN: 0.0296%
- gnomAD_G_NFE: 0.0275%
- Transcripts:
- PCDHA8:ENST00000378123.3:c.159G>A:p.(=)
- PCDHA8:ENST00000531613.1:c.159G>A:p.(=)
- PCDHA8:ENST00000527624.1:c.1602+11787G>A:p.(=)
- PCDHA8:ENST00000529310.1:c.2394+10995G>A:p.(=)
- PCDHA8:ENST00000525929.1:c.2355+4742G>A:p.(=)
- PCDHA8:ENST00000529619.1:c.2352+17353G>A:p.(=)
- PCDHA8:ENST00000529859.1:c.2352+17353G>A:p.(=)
- PCDHA8:ENST00000512229.2:c.2385+31908G>A:p.(=)
- PCDHA8:ENST00000530339.1:c.2385+31908G>A:p.(=)
- PCDHA8:ENST00000526136.1:c.2388+44128G>A:p.(=)
- PCDHA8:ENST00000394633.3:c.1602+53588G>A:p.(=)
- PCDHA8:ENST00000504120.2:c.2394+52796G>A:p.(=)
- PCDHA8:ENST00000522353.2:c.2394+37889G>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 0.1581%
- gnomAD_E_AMR: 0.1267%
- gnomAD_E_EAS: 0.0075%
- gnomAD_E_FIN: 0.0605%
- gnomAD_E_NFE: 0.0718%
- gnomAD_E_OTH: 0.0217%
- gnomAD_E_SAS: 0.0193%
- gnomAD_G_AFR: 0.1074%
- gnomAD_G_EAS: 0.0663%
- gnomAD_G_FIN: 0.0600%
- gnomAD_G_NFE: 0.0279%
- gnomAD_G_OTH: 0.2123%
- Phenotypic similarity 0.432 to Idiopathic pulmonary fibrosis associated with MUC5B.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0100759, Clubbing of fingers
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0100759, Clubbing of fingers
- HP:0010055, Broad hallux - HP:0100759, Clubbing of fingers
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:178500 Pulmonary fibrosis, idiopathic, susceptibility to (susceptibility)
- ORPHA:2032 Idiopathic pulmonary fibrosis (susceptibility)
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.184
- Pathogenicity Data:
- Best Score: 0.41900003
- SIFT: 0.581 (T)
- Frequency Data:
- gnomAD_E_AFR: 0.0198%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_EAS: 0.0767%
- gnomAD_E_NFE: 0.0054%
- gnomAD_E_SAS: 0.0228%
- gnomAD_G_AFR: 0.0577%
- gnomAD_G_EAS: 1.1436%
- gnomAD_G_NFE: 0.0067%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0399%
- TOPMed: 0.0295%
- ExAC EAS: 0.9442%
- ExAC OTH: 0.2146%
- ExAC SAS: 0.0090%
- gnomAD_E_EAS: 0.6938%
- gnomAD_E_OTH: 0.0194%
- gnomAD_E_SAS: 0.0034%
- gnomAD_G_EAS: 1.1714%
- Phenotypic similarity 0.583 to mouse mutant involving AMN.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000157, abnormal sternum morphology
- HP:0001363, Craniosynostosis - MP:0001297, microphthalmia
- HP:0011304, Broad thumb - MP:0000157, abnormal sternum morphology
- HP:0010055, Broad hallux - MP:0000157, abnormal sternum morphology
- Proximity score 0.500 in interactome to CBL and phenotypic similarity 0.642 to Noonan syndrome associated with CBL.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0004209, Clinodactyly of the 5th finger
- HP:0010055, Broad hallux - HP:0001156, Brachydactyly
- Proximity score 0.500 in interactome to CBL and phenotypic similarity 0.299 to mouse mutant of CBL.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001312, abnormal cornea morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:618882 Imerslund-Grasbeck syndrome 2 - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.291
Variant Score: 0.100
- Transcripts:
- AMN:ENST00000299155.5:c.291C>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC EAS: 0.0165%
- ExAC SAS: 0.0078%
- gnomAD_E_EAS: 0.0060%
- gnomAD_E_SAS: 0.0033%
- Phenotypic similarity 0.278 to mouse mutant involving LTN1.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0001312, abnormal cornea morphology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.278
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0030%
- ExAC EAS: 0.0462%
- gnomAD_E_EAS: 0.0580%
- Phenotypic similarity 0.293 to Synaptic congenital myasthenic syndromes associated with LAMB2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - HP:0003691, Scapular winging
- HP:0010055, Broad hallux - HP:0001762, Talipes equinovarus
- Phenotypic similarity 0.340 to mouse mutant involving LAMB2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - MP:0005551, abnormal eye electrophysiology
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Proximity score 0.504 in interactome to LAMA5 and phenotypic similarity 0.739 to mouse mutant of LAMA5.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:609049 Pierson syndrome - autosomal recessive
- OMIM:614199 Nephrotic syndrome, type 5, with or without ocular abnormalities - autosomal recessive
- ORPHA:98915 Synaptic congenital myasthenic syndromes - unknown
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.252
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0019%
- Proximity score 0.503 in interactome to CDC45 and phenotypic similarity 0.703 to Ear-patella-short stature syndrome associated with CDC45.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0004209, Clinodactyly of the 5th finger
- HP:0001363, Craniosynostosis - HP:0001363, Craniosynostosis
- HP:0011304, Broad thumb - HP:0100490, Camptodactyly of finger
- HP:0010055, Broad hallux - HP:0004209, Clinodactyly of the 5th finger
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:616185 Ovarian dysgenesis 4 - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.252
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
- gnomAD_E_EAS: 0.0058%
- Proximity score 0.502 in interactome to FURIN and phenotypic similarity 0.935 to mouse mutant of FURIN.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002544, brachydactyly
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002544, brachydactyly
- HP:0010055, Broad hallux - MP:0002544, brachydactyly
- Proximity score 0.502 in interactome to FURIN and phenotypic similarity 0.274 to fish mutant of FURIN.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly -
- HP:0001363, Craniosynostosis - ZP:0006947, symplectic in contact with Meckel's cartilage, abnormal
- HP:0011304, Broad thumb -
- HP:0010055, Broad hallux -
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:617115 Peeling skin syndrome 5 - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.251
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0004%
- Proximity score 0.503 in interactome to SLC26A2 and phenotypic similarity 0.668 to Atelosteogenesis type II associated with SLC26A2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - HP:0001156, Brachydactyly
- HP:0001363, Craniosynostosis - HP:0001357, Plagiocephaly
- HP:0011304, Broad thumb - HP:0001234, Hitchhiker thumb
- HP:0010055, Broad hallux - HP:0001852, Sandal gap
- Proximity score 0.503 in interactome to SLC26A2 and phenotypic similarity 0.560 to mouse mutant of SLC26A2.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000165, abnormal long bone hypertrophic chondrocyte zone
- HP:0001363, Craniosynostosis - MP:0003419, delayed endochondral bone ossification
- HP:0011304, Broad thumb - MP:0004358, bowed tibia
- HP:0010055, Broad hallux - MP:0004358, bowed tibia
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:214700 Diarrhea 1, secretory chloride, congenital - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.251
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0015%
- ExAC EAS: 0.0813%
- gnomAD_E_EAS: 0.0754%
- Proximity score 0.500 in interactome to CS and phenotypic similarity 0.755 to mouse mutant of CS.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis -
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:212138 Carnitine-acylcarnitine translocase deficiency - autosomal recessive
- ORPHA:159 Carnitine-acylcarnitine translocase deficiency - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.250
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0019%
- Proximity score 0.500 in interactome to MYO10 and phenotypic similarity 0.730 to mouse mutant of MYO10.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0000564, syndactyly
- HP:0001363, Craniosynostosis - MP:0001289, persistence of hyaloid vascular system
- HP:0011304, Broad thumb - MP:0000564, syndactyly
- HP:0010055, Broad hallux - MP:0000564, syndactyly
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:618594 Nephrotic syndrome, type 21 - autosomal recessive
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.250
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
- Proximity score 0.500 in interactome to RABL2B and phenotypic similarity 0.752 to mouse mutant of RABL2B.
- Best Phenotype Matches:
- HP:0001156, Brachydactyly - MP:0002110, abnormal digit morphology
- HP:0001363, Craniosynostosis - MP:0006203, eye hemorrhage
- HP:0011304, Broad thumb - MP:0002110, abnormal digit morphology
- HP:0010055, Broad hallux - MP:0002110, abnormal digit morphology
- Known diseases - observed variants incompatible with mode of inheritance:
- OMIM:612551 End-stage renal disease, nondiabetic, susceptibility to (susceptibility)
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.250
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0399%
- TOPMed: 0.0072%
- ESP AA: 0.0227%
- ESP All: 0.0077%
- ExAC AFR: 0.0288%
- ExAC NFE: 0.0045%
- gnomAD_E_AFR: 0.0261%
- gnomAD_E_FIN: 0.0045%
- gnomAD_E_NFE: 0.0054%
- gnomAD_G_AFR: 0.0115%
- No phenotype or PPI evidence
X_RECESSIVE
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.309
- Pathogenicity Data:
- Best Score: 0.784
- Polyphen2: 0.659 (P)
- SIFT: 0.216 (T)
- Frequency Data:
- 1000Genomes: 0.1325%
- TOPMed: 0.0385%
- ExAC AMR: 0.0107%
- ExAC EAS: 1.2975%
- ExAC SAS: 0.0297%
- gnomAD_E_EAS: 1.1351%
- gnomAD_E_OTH: 0.0494%
- gnomAD_E_SAS: 0.0419%
- gnomAD_G_EAS: 1.7013%
- No phenotype or PPI evidence
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.294
- Transcripts:
- CRYBG3:ENST00000182096.4:c.1698C>G:p.(His566Gln)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.1398%
- TOPMed: 0.0552%
- ExAC EAS: 0.7452%
- ExAC NFE: 0.0030%
- ExAC SAS: 0.0121%
- gnomAD_E_EAS: 0.7579%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_SAS: 0.0071%
- gnomAD_G_EAS: 0.8663%
- gnomAD_G_NFE: 0.0067%
- Transcripts:
- CRYBG3:ENST00000182096.4:c.1503C>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.100
- Transcripts:
- CRYBG3:ENST00000182096.4:c.1503C>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.273
- Pathogenicity Data:
- Best Score: 0.978
- Polyphen2: 0.677 (P)
- SIFT: 0.022 (D)
- Frequency Data:
- 1000Genomes: 0.3594%
- TOPMed: 0.0680%
- ExAC EAS: 1.4830%
- ExAC NFE: 0.0046%
- ExAC SAS: 0.0069%
- gnomAD_E_EAS: 1.5688%
- gnomAD_E_NFE: 0.0037%
- gnomAD_E_SAS: 0.0241%
- gnomAD_G_EAS: 1.6069%
- Transcripts:
- XIRP2:ENST00000295237.9:c.10449G>A:p.(=)
- XIRP2:ENST00000409195.1:c.10449G>A:p.(=)
- XIRP2:ENST00000409273.1:c.9783G>A:p.(=)
- XIRP2:ENST00000409043.1:c.1177-2191G>A:p.(=)
- XIRP2:ENST00000409605.1:c.511-2191G>A:p.(=)
- XIRP2:ENST00000409728.1:c.1276-2191G>A:p.(=)
- XIRP2:ENST00000409756.2:c.1177-2191G>A:p.(=)
- XIRP2:ENST00000420519.1:c.1276-2191G>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0599%
- TOPMed: 0.0094%
- UK10K: 0.0132%
- ESP EA: 0.0122%
- ESP All: 0.0084%
- ExAC EAS: 0.1398%
- ExAC NFE: 0.0151%
- ExAC SAS: 0.0367%
- gnomAD_E_AMR: 0.0060%
- gnomAD_E_EAS: 0.2962%
- gnomAD_E_NFE: 0.0118%
- gnomAD_E_SAS: 0.0456%
- gnomAD_G_AMR: 0.1196%
- gnomAD_G_EAS: 0.2541%
- No phenotype or PPI evidence
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.269
- Transcripts:
- TEKT4P2:ENST00000416067.1:n.130-2A>T:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_G_AFR: 0.7353%
- gnomAD_G_AMR: 1.7544%
- gnomAD_G_EAS: 1.1765%
- gnomAD_G_FIN: 1.8499%
- gnomAD_G_NFE: 1.0155%
- gnomAD_G_OTH: 0.6623%
- Transcripts:
- TEKT4P2:ENST00000416067.1:n.130-5C>T:
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_G_AFR: 0.7991%
- gnomAD_G_AMR: 1.7857%
- gnomAD_G_EAS: 1.2821%
- gnomAD_G_FIN: 1.5963%
- gnomAD_G_NFE: 1.1327%
- gnomAD_G_OTH: 0.6849%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.100
- Transcripts:
- GPLD1:ENST00000230036.1:c.2454T>C:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.100
- Transcripts:
- RALGAPA2:ENST00000202677.7:c.5445C>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- No frequency data
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.100
- Transcripts:
- C10orf12:ENST00000286067.2:c.1215G>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.100
- Transcripts:
- FAM189A1:ENST00000261275.4:c.852T>C:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0004%
- gnomAD_E_AMR: 0.0030%
- No phenotype or PPI evidence
- Known diseases:
- OMIM:601583 Wilms tumor susceptibility-5 (susceptibility)
- ORPHA:654 Nephroblastoma (susceptibility)
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
- ExAC AMR: 0.0087%
- ExAC NFE: 0.0015%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_NFE: 0.0009%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.100
- Transcripts:
- CDC42BPG:ENST00000342711.5:c.2091C>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0011%
- gnomAD_E_EAS: 0.0116%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.100
- Transcripts:
- RNPEPL1:ENST00000270357.4:c.855G>A:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0034%
- gnomAD_E_EAS: 0.0117%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_SAS: 0.0033%
- gnomAD_G_NFE: 0.0134%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0024%
- ESP EA: 0.0116%
- ESP All: 0.0077%
- ExAC AFR: 0.0101%
- ExAC NFE: 0.0061%
- ExAC SAS: 0.0061%
- gnomAD_E_AFR: 0.0066%
- gnomAD_E_EAS: 0.0058%
- gnomAD_E_NFE: 0.0063%
- gnomAD_E_OTH: 0.0183%
- gnomAD_E_SAS: 0.0033%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.100
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0023%
- ExAC EAS: 0.0232%
- gnomAD_E_EAS: 0.0348%
- gnomAD_E_SAS: 0.0032%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.099
- Transcripts:
- KRTAP5-2:ENST00000412090.1:c.78T>C:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_FIN: 0.0284%
- gnomAD_E_NFE: 0.0426%
- gnomAD_E_OTH: 0.0380%
- gnomAD_E_SAS: 0.0443%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.052
- Transcripts:
- KRTAP5-2:ENST00000412090.1:c.78T>C:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_FIN: 0.0284%
- gnomAD_E_NFE: 0.0426%
- gnomAD_E_OTH: 0.0380%
- gnomAD_E_SAS: 0.0443%
- Transcripts:
- KRTAP5-2:ENST00000412090.1:c.58A>G:p.(Ser20Gly)
- Pathogenicity Data:
- Best Score: 0.005
- Polyphen2: 0.005 (B)
- Frequency Data:
- gnomAD_E_AFR: 0.0135%
- gnomAD_E_AMR: 0.0213%
- gnomAD_E_FIN: 0.0767%
- gnomAD_E_NFE: 0.1038%
- gnomAD_E_OTH: 0.1151%
- gnomAD_E_SAS: 0.1383%
- gnomAD_G_AFR: 0.0708%
- gnomAD_G_AMR: 0.3049%
- gnomAD_G_EAS: 0.0761%
- gnomAD_G_FIN: 0.3261%
- gnomAD_G_NFE: 0.2889%
- gnomAD_G_OTH: 0.1235%
- Transcripts:
- KRTAP5-2:ENST00000412090.1:c.22A>G:p.(Arg8Gly)
- Pathogenicity Data:
- Best Score: 0.0
- Polyphen2: 0.000 (B)
- Frequency Data:
- 1000Genomes: 0.0399%
- TOPMed: 0.0399%
- gnomAD_E_AFR: 0.0601%
- gnomAD_G_AFR: 0.0234%
- gnomAD_G_EAS: 0.0637%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0023%
- ExAC EAS: 0.0116%
- ExAC NFE: 0.0015%
- gnomAD_E_EAS: 0.0581%
- gnomAD_E_NFE: 0.0009%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0599%
- TOPMed: 0.0079%
- ExAC AFR: 0.0099%
- ExAC EAS: 0.0231%
- ExAC NFE: 0.0015%
- gnomAD_E_AFR: 0.0131%
- gnomAD_E_EAS: 0.0175%
- gnomAD_E_NFE: 0.0018%
- gnomAD_G_NFE: 0.0067%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.099
- Transcripts:
- ARNTL2:ENST00000261178.5:c.1527A>C:p.(=)
- ARNTL2:ENST00000266503.5:c.1671A>C:p.(=)
- ARNTL2:ENST00000311001.5:c.1629A>C:p.(=)
- ARNTL2:ENST00000395901.2:c.1560A>C:p.(=)
- ARNTL2:ENST00000542388.1:c.1416A>C:p.(=)
- ARNTL2:ENST00000544915.1:c.1569A>C:p.(=)
- ARNTL2:ENST00000546179.1:c.1554+2146A>C:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0008%
- gnomAD_E_EAS: 0.0117%
- gnomAD_G_EAS: 0.0617%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0004%
- ExAC EAS: 0.0231%
- gnomAD_E_EAS: 0.0174%
- gnomAD_G_EAS: 0.0617%
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0004%
- ExAC EAS: 0.0231%
- gnomAD_E_EAS: 0.0174%
- gnomAD_G_EAS: 0.0617%
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- ExAC EAS: 0.0231%
- gnomAD_E_EAS: 0.0174%
- gnomAD_G_EAS: 0.0617%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0094%
- gnomAD_E_AMR: 0.0084%
- gnomAD_E_EAS: 0.0587%
- gnomAD_E_NFE: 0.0019%
- gnomAD_G_EAS: 0.0617%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.099
- Transcripts:
- TMEM133:ENST00000303130.2:c.258C>T:p.(=)
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0200%
- ExAC EAS: 0.0116%
- gnomAD_E_AFR: 0.0131%
- gnomAD_E_EAS: 0.0116%
- gnomAD_G_EAS: 0.0618%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0223%
- ESP AA: 0.0454%
- ESP All: 0.0154%
- ExAC AFR: 0.0673%
- ExAC EAS: 0.0463%
- ExAC SAS: 0.0061%
- gnomAD_E_AFR: 0.0653%
- gnomAD_E_AMR: 0.0089%
- gnomAD_E_EAS: 0.0464%
- gnomAD_E_NFE: 0.0009%
- gnomAD_E_OTH: 0.0183%
- gnomAD_E_SAS: 0.0032%
- gnomAD_G_AFR: 0.0115%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.099
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- TOPMed: 0.0272%
- ESP AA: 0.0227%
- ESP All: 0.0077%
- ExAC AFR: 0.0683%
- gnomAD_E_AFR: 0.0788%
- gnomAD_E_AMR: 0.0030%
- gnomAD_E_NFE: 0.0009%
- gnomAD_G_AFR: 0.0805%
- No phenotype or PPI evidence
AUTOSOMAL_RECESSIVE
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.063
- Pathogenicity Data:
- No pathogenicity data
- Frequency Data:
- gnomAD_E_AFR: 1.1911%
- gnomAD_E_AMR: 0.1741%
- gnomAD_E_EAS: 0.0120%
- gnomAD_E_FIN: 0.0314%
- gnomAD_E_NFE: 0.0788%
- gnomAD_E_OTH: 0.0368%
- gnomAD_E_SAS: 0.1701%
- gnomAD_G_AFR: 0.8479%
- gnomAD_G_AMR: 0.6276%
- gnomAD_G_EAS: 0.2252%
- gnomAD_G_FIN: 1.3185%
- gnomAD_G_NFE: 0.5303%
- gnomAD_G_OTH: 0.8811%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.000
- Pathogenicity Data:
- Best Score: 0.0
- Polyphen2: 0.000 (B)
- Frequency Data:
- TOPMed: 0.0030%
- gnomAD_E_AMR: 0.0047%
- gnomAD_E_NFE: 0.0079%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.000
- Pathogenicity Data:
- Best Score: 0.0
- SIFT: 1.000 (T)
- Frequency Data:
- gnomAD_E_EAS: 0.0140%
- gnomAD_E_FIN: 0.0402%
- gnomAD_E_NFE: 0.0029%
- gnomAD_E_SAS: 0.0087%
- gnomAD_G_AFR: 0.0659%
- gnomAD_G_EAS: 0.0797%
- gnomAD_G_FIN: 0.0634%
- gnomAD_G_NFE: 0.0143%
- No phenotype or PPI evidence
AUTOSOMAL_DOMINANT
Exomiser Score: 0.000
Phenotype Score: 0.000
Variant Score: 0.000
- Pathogenicity Data:
- Best Score: 0.0
- Polyphen2: 0.000 (B)
- Frequency Data:
- 1000Genomes: 0.0200%
- TOPMed: 0.0212%
- gnomAD_E_AFR: 0.0458%
- gnomAD_E_NFE: 0.0009%
- gnomAD_G_AFR: 0.0574%
About
The Exomizer is a Java program that functionally annotates variants from whole-exome sequencing data starting from a VCF file (version 4). The functional annotation code is based on Jannovar and uses UCSC KnownGene transcript definitions and hg19 genomic coordinates
Variants are prioritized according to user-defined criteria on variant frequency, pathogenicity, quality, inheritance pattern, and model organism phenotype data. Predicted pathogenicity data was extracted from the dbNSFP resource.
Developed by the Computational Biology and Bioinformatics group at the Institute for Medical Genetics and Human Genetics of the Charité - Universitätsmedizin Berlin, the Mouse Informatics Group at the Sanger Institute and the Smedley group at Queen Mary University of London.
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